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Feline Array PAG 2016

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This is my talk at the plant and animal genome conference. The talk discusses the feline snp array and its usefulness for feline genetics studies

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Feline Array PAG 2016

  1. 1. The Feline SNP Array Features and Utility Hasan Alhaddad, Ph.D. Kuwait University
  2. 2. Barbara Gandolfi Hasan Alhaddad Mike Montague 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. 3. AIMS • Share information of the available dataset of genotyped cats • Provide an updated version of Feline SNP array • Analyze basic population genetics of available genotype dataset • Initiate and encourage collaborations based on the available genotype dataset
  4. 4. Outline • Introduction • Genotype dataset • Feline array features • Array utility
  5. 5. Cat genome & SNPs Mullikin et al. BMC Genomics 2010, 11:406 http://www.biomedcentral.com/1471-2164/11/406 Open AccessDATABASE Database Light whole genome sequence for SNP discovery across domestic cat breeds James C Mullikin*1, Nancy F Hansen1, Lei Shen2, Heather Ebling2, William F Donahue2, Wei Tao2, David J Saranga2, Adrianne Brand2, Marc J Rubenfield2, Alice C Young1, Pedro Cruz1 for NISC Comparative Sequencing Program1, Carlos Driscoll3, Victor David3, Samer WK Al-Murrani4, Mary F Locniskar4, Mitchell S Abrahamsen4, Stephen J O'Brien3, Douglas R Smith2 and Jeffrey A Brockman4 Abstract Background: The domestic cat has offered enormous genomic potential in the veterinary description of over 250 hereditary disease models as well as the occurrence of several deadly feline viruses (feline leukemia virus -- FeLV, feline coronavirus -- FECV, feline immunodeficiency virus - FIV) that are homologues to human scourges (cancer, SARS, and AIDS respectively). However, to realize this bio-medical potential, a high density single nucleotide polymorphism (SNP) map is required in order to accomplish disease and phenotype association discovery. Description: To remedy this, we generated 3,178,297 paired fosmid-end Sanger sequence reads from seven cats, and combined these data with the publicly available 2X cat whole genome sequence. All sequence reads were assembled together to form a 3X whole genome assembly allowing the discovery of over three million SNPs. To reduce potential false positive SNPs due to the low coverage assembly, a low upper-limit was placed on sequence coverage and a high lower-limit on the quality of the discrepant bases at a potential variant site. In all domestic cats of different breeds: female Abyssinian, female American shorthair, male Cornish Rex, female European Burmese, female Persian, female Siamese, a male Ragdoll and a female African wildcat were sequenced lightly. We report a total of 964 k common SNPs suitable for a domestic cat SNP genotyping array and an additional 900 k SNPs detected between African wildcat and domestic cats breeds. An empirical sampling of 94 discovered SNPs were tested in the sequenced cats resulting in a 10.1101/gr.6380007Access the most recent version at doi: 2007 17: 1675-1689Genome Res. Bourque, Glenn Tesler, NISC Comparative Sequencing Program and Stephen J. O’Brien Antunes, Marilyn Menotti-Raymond, Naoya Yuhki, Jill Pecon-Slattery, Warren E. Johnson, Guillaume A. Schäffer, Richa Agarwala, Kristina Narfström, William J. Murphy, Urs Giger, Alfred L. Roca, Agostinho Sante Gnerre, Michele Clamp, Jean Chang, Robert Stephens, Beena Neelam, Natalia Volfovsky, Alejandro Joan U. Pontius, James C. Mullikin, Douglas R. Smith, Agencourt Sequencing Team, Kerstin Lindblad-Toh, Initial sequence and comparative analysis of the cat genome data Supplementary http://www.genome.org/cgi/content/full/17/11/1675/DC1 "Supplemental Research Data" References http://www.genome.org/cgi/content/full/17/11/1675#References This article cites 97 articles, 41 of which can be accessed free at: service Email alerting click heretop right corner of the article or Receive free email alerts when new articles cite this article - sign up in the box at the Notes http://www.genome.org/subscriptions/ go to:Genome ResearchTo subscribe to © 2007 Cold Spring Harbor Laboratory Press on November 5, 2007www.genome.orgDownloaded from Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication Michael J. Montaguea,1 , Gang Lib,1 , Barbara Gandolfic , Razib Khand , Bronwen L. Akene , Steven M. J. Searlee , Patrick Minxa , LaDeana W. Hilliera , Daniel C. Koboldta , Brian W. Davisb , Carlos A. Driscollf , Christina S. Barrf , Kevin Blackistonef , Javier Quilezg , Belen Lorente-Galdosg , Tomas Marques-Bonetg,h , Can Alkani , Gregg W. C. Thomasj , Matthew W. Hahnj , Marilyn Menotti-Raymondk , Stephen J. O’Brienl,m , Richard K. Wilsona , Leslie A. Lyonsc,2 , William J. Murphyb,2 , and Wesley C. Warrena,2 a The Genome Institute, Washington University School of Medicine, St. Louis, MO 63108; b Department of Veterinary Integrative Biosciences, College of Veterinary Medicine, Texas A&M University, College Station, TX 77843; c Department of Veterinary Medicine & Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO 65201; d Population Health & Reproduction, School of Veterinary Medicine, University of California, Davis, CA 95616; e Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom; f National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, g
  6. 6. Cat SNPs • Marker selected based on: • Re-sequencing of Cinnamon • Sequencing 7 discovery cats • Sequencing 6 breeds + random bred population + wild cat (pooled individuals).
  7. 7. Array • Illumina Infinium iSelect 63K Cat DNA array • Released 2011 http://felinegenetics.missouri.edu/feline-genome-project-2/cat-genomic-resources-strs-snps
  8. 8. • Introduction • Genotype dataset • Feline array features • Array’s utility • Genotype dataset Outline
  9. 9. Samples Breed (1824) Random bred (262) Domestic European wildcats Asian Leopard cats Big cats Non-Pedigree Lyons Ped (139) LxD Ped (81) Toyger (34) Lykoi Ped (27) T.Rex Ped (21) • > 2000 Domestic cats • > 50 wild cats (different species) • 5 pedigrees • 262 ramdom bred cats • > 1800 pedigreed breed cats
  10. 10. Samples Sample size 0 50 100 150 200 250 300 Abyssinian American Curl American Shorthair American Wirehair Bengal Birman Bombay British Shorthair Burmese Chartreaux Cornish Rex Devon Rex Egyptian Mau Havana Brown Japanese Bobtail Khoa Manee Korat Kurillian Bobtail La Perm Lykoi Maine Coon Manx Munchkin Norweigian Forest Cat Ocicat Oriental Perisan Peterbald Ragdoll Russian Blue Scottish Fold Selkirk Rex Siamese Siberian Singapura Somali Sphynx Tennesse REX Turkish Angora Turkish Van 40 breeds Average 39 cats/breed 22 breeds > 20 individuals
  11. 11. • Introduction • Genotype dataset • Feline array features • Array’s utility • Feline array features Outline
  12. 12. Array’s features Autosomal X-linked Unassigned (~ 11%) (~ 4.5%) Domestic Wildcat (~ 6.5%) Non-phenotypic Phenotypic (~ 0.05%) Non-phylogenetic Phylogenetic (~ 0.15%) • ~ 63K SNPs. • Domestic cat SNPs • Wildcat SNPs • Autosomal • X-linked • Phenotypic • Phylogentic • ~11% unknown location !!!
  13. 13. Array’s features ~ 11% of SNPs unassigned to genomic location (rs397514112). Genotyping was performed as described (Table S1). Analysis employed the mixed model or glim- mix procedure in SAS v9.2 (SAS Institute) as described.6,7 For each analysis, the production trait of interest was included as the dependent variable. Other model terms included breed, sire, year of birth, age in years, age at last lambing and genotype as described (Appendix S1). Bonfer- roni correction accounted for multiple testing. Comments: The ZNF389 deletion variant was not consis- tently associated with any tested production traits between lifetime and partial-lifetime SRLV-negative groups (Tables S1 and S4). Insertion homozygotes previously associated with reduced SRLV proviral concentration were associated with lower birth weight in the partial-lifetime group (Bon- ferroni P = 0.033; Table S4), but the weight difference was small (0.41 kg) and not replicated in the lifetime group (nominal P = 0.41; Table S2). Further, there was no associ- ation with weaning or later weights (Tables S2 and S4). These results showed no consistent association of the ZNF389 deletion variant with ewe lifetime production. Other breeds and additional traits, such as wool diameter and infectious disease traits besides control of SRLV, should be examined to more fully assess this locus. Acknowledgements: Thanks to James Reynolds, Caylee Birge, Codie Durfee, Nic Durfee, Liam Broughton-Neiswanger, Ralph Horn, James Allison, Tom Kellom, Natalie Pierce, Mark Williams and USSES farm crew for technical assis- tance. This work was supported by USDA-ARS Grant 5348-32000-031-00D. Conflict of interest: The authors have no conflict of interest to declare. References 1 White S.N. et al. (2012) PLoS One 7, e47829. 2 White S.N. et al. (2014) Anim Genet 45, 297–300. 3 Herrmann-Hoesing L.M. et al. (2009) Clin Vaccine Immunol 16, 551–7. 4 White S.N. & Knowles D.P. (2013) Viruses 5, 1466–99. 5 Herrmann-Hoesing L.M. et al. (2007) Clin Vaccine Immunol 14, 1274–8. 6 Mousel M.R. et al. (2010) Anim Genet 41, 222–3. tive ewes. Table S3 ZNF389 deletion variant genotype counts among partial-lifetime group SRLV-negative ewes. Table S4 Association results between ZNF389 deletion variant and production phenotypes among partial-lifetime group SRLV-negative ewes. doi: 10.1111/age.12169 An updated felCat5 SNP manifest for the Illumina Feline 63k SNP genotyping array Cali E. Willet and Bianca Haase Faculty of Veterinary Science, University of Sydney, Sydney, NSW, 2006, Australia Accepted for publication 01 April 2014 Background: The development of the first Illumina Infinium iSelect 63k Cat DNA genotyping array has been a mile- stone in feline research. Since its release in February 2011, the International Cat Genome Sequencing Consor- tium released a new version of the feline genome assembly (Felis_catus 6.2/felCat5; GenBank assembly ID GCA_000181335.2). As inconsistencies between genome assemblies can complicate genome-wide association stud- ies, we compare SNP locations of the manifest provided with the Illumina Infinium iSelect 63k Cat DNA genotyp- ing array with the most recent feline genome assembly, felCat5. We make the resultant updated SNP manifest available to the cat research community. Methods: A FASTA file was created using the SNP identifier and the genomic sequence in top orientation from the cur- rent feline SNP manifest. For each probe, the longest of the two flanking sequences either side of the variant was selected to create the BLAST input file, and a nucleotide basic local alignment search (BLAST)1 against the Felis_ca- tus 6.2/felCat5 whole-genome assembly, September 2011 build, downloaded from UCSC Genome Browser (http:// Table 2 Ten most associated markers obtained by genome-wide analyses of Persian PRA No. Chr. SNP ID Position TDT sib-TDT Case–control Praw Pgenome Praw Pgenome Praw Pgenome 1 E1 chrUn5.6839723 1831172 4.32E-08 1.00E-05 1.00E-05 0.1632 7.64E-13 1.00E-05 2 E1 chrUn5.6133983 1106562 1.21E-07 0.00013 0.00013 0.4071 1.52E-10 1.00E-05 3 E1 chrUn5.6766609 1751066 5.73E-07 0.00282 0.00282 0.5451 2.97E-09 5.00E-05 4 E1 chrUn5.6481762 1452354 7.74E-06 0.06134 0.06134 0.9057 2.70E-07 0.00226 5 E1 chrUn5.6503134 1476010 2.21E-05 0.1905 0.1905 0.9644 1.15E-06 0.00841 6 E1 chrUn5.5846986 808916 3.74E-05 0.3135 0.3135 0.9487 4.65E-06 0.03121 7 E1 chrUn5.6185290 1154788 3.74E-05 0.3135 0.3135 0.9487 8.04E-06 0.05255 8 E1 chrUn5.6912692 1912858 3.74E-05 0.3135 0.3135 0.9793 – – 9 E1 chrUn5.6942249 1932982 3.74E-05 0.3135 0.3135 0.9793 5.95E-06 0.03955 10 E1 chrUn5.7293975 2293660 3.74E-05 0.3135 0.3135 0.9487 8.76E-07 0.00658 11 F1 chrUn5.7948667 2997440 – – – – 4.45E-06 0.02986 Genome-wide analyses of Persian PRA Genome-wide association and linkage analyses localize a progressive retinal atrophy locus in Persian cats Hasan Alhaddad • Barbara Gandolfi • Robert A. Grahn • Hyung-Chul Rah • Carlyn B. Peterson • David J. Maggs • Kathryn L. Good • Niels C. Pedersen • Leslie A. Lyons Received: 19 February 2014 / Accepted: 3 April 2014 Ó The Author(s) 2014. This article is published with open access at Springerlink.com Abstract Hereditary eye diseases of animals serve as excellent models of human ocular disorders and assist in the development of gene and drug therapies for inherited forms of blindness. Several primary hereditary eye condi- tions affecting various ocular tissues and having different rates of progression have been documented in domestic cats. Gene therapy for canine retinopathies has been suc- cessful, thus the cat could be a gene therapy candidate for other forms of retinal degenerations. The current study investigates a hereditary, autosomal recessive, retinal degeneration specific to Persian cats. A multi-generational pedigree segregating for this progressive retinal atrophy was genotyped using a 63 K SNP array and analyzed via genome-wide linkage and association methods. A multi- point parametric linkage analysis localized the blindness phenotype to a *1.75 Mb region with significant LOD scores (Z & 14, h = 0.00) on cat chromosome E1. Gen- ome-wide TDT, sib-TDT, and case–control analyses also consistently supported significant association within the same region on chromosome E1, which is homologous to human chromosome 17. Using haplotype analysis, a *1.3 Mb region was identified as highly associated for progressive retinal atrophy in Persian cats. Several candi- date genes within the region are reasonable candidates as a potential causative gene and should be considered for molecular analyses. Introduction The eye is a highly complex organ comprised of several highly specialized cells. The development, structure, and function of the eye involves the interaction of thousands of genes. Genetic mutations in genes involving the eye are likely to be detrimental to the fitness of cats, especially Mamm Genome DOI 10.1007/s00335-014-9517-z Table 2 Ten most associated markers obtained by genome-wide analyses of Persian PRA No. Chr. SNP ID Position TDT sib-TDT Case–control Praw Pgenome Praw Pgenome Praw Pgenome 1 E1 chrUn5.6839723 1831172 4.32E-08 1.00E-05 1.00E-05 0.1632 7.64E-13 1.00E-05 2 E1 chrUn5.6133983 1106562 1.21E-07 0.00013 0.00013 0.4071 1.52E-10 1.00E-05 3 E1 chrUn5.6766609 1751066 5.73E-07 0.00282 0.00282 0.5451 2.97E-09 5.00E-05 4 E1 chrUn5.6481762 1452354 7.74E-06 0.06134 0.06134 0.9057 2.70E-07 0.00226 5 E1 chrUn5.6503134 1476010 2.21E-05 0.1905 0.1905 0.9644 1.15E-06 0.00841 6 E1 chrUn5.5846986 808916 3.74E-05 0.3135 0.3135 0.9487 4.65E-06 0.03121 7 E1 chrUn5.6185290 1154788 3.74E-05 0.3135 0.3135 0.9487 8.04E-06 0.05255 8 E1 chrUn5.6912692 1912858 3.74E-05 0.3135 0.3135 0.9793 – – 9 E1 chrUn5.6942249 1932982 3.74E-05 0.3135 0.3135 0.9793 5.95E-06 0.03955 10 E1 chrUn5.7293975 2293660 3.74E-05 0.3135 0.3135 0.9487 8.76E-07 0.00658 11 F1 chrUn5.7948667 2997440 – – – – 4.45E-06 0.02986 Genome-wide analyses of Persian PRA
  14. 14. Remapping and distances • Remapping SNPs to genomic locations on genome assembly 8.0. • Majority of SNPs are < 50Kb apart.
  15. 15. Mendelian errors Percent Markers with Mendelian Errors 0 2 4 6 8 10 020 a. 0 0100002 b. A1 A2 A3 B1 B2 B3 B4 C1 C2 D1 D2 D3 D4 E1 E2 E3 F1 F2 UN X Chromosome No.ofSNPs 051015202530 c. No.ofSNPs 0 02004006008001000 d. Evaluating Mendelian inheritance in 83 Trios 10 Percent Mendelian Errors NumberofSNPs 0 20 40 60 80 0100002000030000400005000060000 b.
  16. 16. SNP information update •New SNP locations based on 8.0 cat genome assembly • Removal of SNPs with low genotyping rate • Removal/marking SNPs with significant Mendelian errors.
  17. 17. Final SNP-set A1 A2 A3 B1 B2 B3 B4 C1 C2 D1 D2 D3 D4 E1 E2 E3 F1 F2 X UN Chromosome NumberofSNPs 01000200030004000500060007000 Assigned Un-assigned (~ 1%) Included Exluded (~ 1%) Less than 1% SNPs excluded due to low genotyping rate Less than 1% SNPs remains unassigned Final SNP number is 62272
  18. 18. • Introduction • Genotype dataset • Feline array features • Array’s utility • Population genetics of cats • GWAS • Selection and breed history • Array’s utility • Population genetics of cats • GWAS • Selection and breed history Outline
  19. 19. Monomorphic ABY ACURL ASH Asian BEN BIR BOM BSH BUR CHR Colony CREX DREX DOM EGY HAV HYD JBOB MANEE KOR KBOB PERM LYK MCOON MANX MUNCH NFC OCI ORI PER PBALD RAG RBLUE SFOLD SREX SIA SIR SIN SOM SPH TREX ANG VAN ALC WIR BIGW XPED FSI 0 10000 20000 30000 40000 50000 60000 No.SNPs A1 A2 A3 B1 B2 B3 B4 C1 C2 D1 D2 D3 D4 E1 E2 E3 F1 F2 X Pretty graph with low information value
  20. 20. Population structure -0.10 -0.05 0.00 0.05 0.10 0.15 -0.06-0.04-0.020.000.020.04 Dimesnion 1 Dimension2 Persian Selkirk Rex British Shorthair Scotish Fold Manx Siberian Sphynx Abyssinian Turkish Angora Turkish Van J. Bobtail Cornish Rex Bengal Ocicat Oriental cats Siamese Burmese Korat Birman a. East-West breed genetic structure
  21. 21. Linkage disequilibrium 0 1 2 3 4 0.00.10.20.30.40.5 Pairwise-SNPs Distace (MB) MeanSquaredCorrelationCoefficient(r2 ) Random Bred Max Random Bred (r2 ) a. Extent of LD (Kb) 0 500 1000 1500 b. Persian Slekirk Rex British shorthair Scottish Fold Maine Coon Abyssinian Turkish Van Bengal Munchikan LaPerm Devon Rex Ragdoll American Curl Siberian Sphynx Peterbald Oriental Siamese Burmese Birman EU wild • LD ranges (50Kb - 1.5MB) • Eastern breeds higher LD • Local LD vs. genome-wide LD Alhaddad, H., et al. (2013). "Extent of linkage disequilibrium in the domestic cat, Felis silvestris catus, and its breeds." PloS one 8(1): e53537.
  22. 22. Runs of homozygosity Birman Burmese Siamese Oriental Peterbald Sphynx Siberian American Curl Ragdoll Devon Rex LaPerm Munchikan Bengal Turkish Van Abyssinian Maine Coon Scottish Fold British shorthair Slekirk Rex Persian 28 8 25 14 17 81 4 9 3 5 25 20 9 4 8 28 94 129 238 177 a. Total Number 21 5 14 8 11 48 3 5 3 2 14 14 7 3 3 16 63 82 156 93 b. < 500 Kb 3 2 9 5 5 20 1 3 0 2 9 3 1 0 3 9 18 34 50 40 c. 500 Kb - 1000 Kb 4 1 2 1 1 13 0 1 0 1 2 3 1 1 2 3 13 13 32 44 d. > 1000 Kb
  23. 23. GWAS Trait: Dilute color Population: Random bred Cases: 33 Controls: 81 Haplotype: NA Causative SNP: on chip
  24. 24. GWAS Sample size = 114 r2 = 0.26 Distance = 4.4 Kb Needed sample size = 427 -2 -1 0 1 2 0.0 0.2 0.4 0.6 0.8 1.0 Distance (Mb) SquaredCorrelationCoefficient(r2 ) Pritchard and Przeworski: Linkage Disequilibrium in Humans 910 Am. J. Hum. Genet. 69:1–14, 2001
  25. 25. GWAS Trait: Long hair Population: LaPerm breed Cases: 32 Controls: 22 Haplotype: ~ 150 Kb Causative SNP: on chip
  26. 26. GWAS -3 -2 -1 0 1 2 3 0.0 0.2 0.4 0.6 0.8 1.0 Distance (Mb) SquaredCorrelationCoefficient(r2 ) Sample size = 54 r2 = 0.81 Distance = 1 Kb Needed sample size = 66
  27. 27. GWAS Trait: Point color Population: Persian breed Cases: 21 Controls: 28 Haplotype: ~ 1Mb Causative SNP: on chip
  28. 28. GWAS -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 0.0 0.2 0.4 0.6 0.8 1.0 Distance (Mb) SquaredCorrelationCoefficient(r2 ) Sample size = 49 r2 = 0.98 Distance = 55 Kb Needed sample size = 50
  29. 29. GWAS Trait: Orange color Population: Random bred Cases: 24 Controls: 69 Haplotype: ~ 1.5 Mb Causative variant unknown
  30. 30. GWAS First WNK4-Hypokalemia Animal Model Identified by Genome-Wide Association in Burmese Cats Barbara Gandolfi1 , Timothy J. Gruffydd-Jones2 , Richard Malik3 , Alejandro Cortes1 , Boyd R. Jones4 , Chris R. Helps5 , Eva M. Prinzenberg6 , George Erhardt6 , Leslie A. Lyons1 1 Department of Population Health and Reproduction, University of California Davis, Davis, California, United States of America, 2 The Feline Centre, University of Bristol, Langford, Bristol, United Kingdom, 3 Centre for Veterinary Education, University of Sydney, Sydney, Australia, 4 Institute of Veterinary, Animal & Biomedical Sciences, Massey University, Palmerston North, New Zealand, 5 Molecular Diagnostic Unit, University of Bristol, Langford, Bristol, United Kingdom, 6 Institute of Animal Breeding & Genetics, Justus Liebig University, Giessen, Germany Abstract Burmese is an old and popular cat breed, however, several health concerns, such as hypokalemia and a craniofacial defect, are prevalent, endangering the general health of the breed. Hypokalemia, a subnormal serum potassium ion concentration ([K+ ]), most often occurs as a secondary problem but can occur as a primary problem, such as hypokalaemic periodic paralysis in humans, and as feline hypokalaemic periodic polymyopathy primarily in Burmese. The most characteristic clinical sign of hypokalemia in Burmese is a skeletal muscle weakness that is frequently episodic in nature, either generalized, or sometimes localized to the cervical and thoracic limb girdle muscles. Burmese hypokalemia is suspected to be a single locus autosomal recessive trait. A genome wide case-control study using the illumina Infinium Feline 63K iSelect DNA array was performed using 35 cases and 25 controls from the Burmese breed that identified a locus on chromosome E1 associated with hypokalemia. Within approximately 1.2 Mb of the highest associated SNP, two candidate genes were identified, KCNH4 and WNK4. Direct sequencing of the genes revealed a nonsense mutation, producing a premature stop codon within WNK4 (c.2899C.T), leading to a truncated protein that lacks the C-terminal coiled-coil domain and the highly conserved Akt1/SGK phosphorylation site. All cases were homozygous for the mutation. Although the exact mechanism causing hypokalemia has not been determined, extrapolation from the homologous human and mouse genes suggests the mechanism may involve a potassium-losing nephropathy. A genetic test to screen for the genetic defect within the active breeding population has been developed, which should lead to eradication of the mutation and improved general health within the breed. Moreover, the identified mutation may help clarify the role of the protein in K+ regulation and the cat represents the first animal model for WNK4-associated hypokalemia. Citation: Gandolfi B, Gruffydd-Jones TJ, Malik R, Cortes A, Jones BR, et al. (2012) First WNK4-Hypokalemia Animal Model Identified by Genome-Wide Association in Burmese Cats. PLoS ONE 7(12): e53173. doi:10.1371/journal.pone.0053173 Editor: Yann Herault, IGBMC/ICS, France Received August 14, 2012; Accepted November 26, 2012; Published December 28, 2012 Copyright: ß 2012 Gandolfi et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This work was supported by funding from the National Center for Research Resources R24 RR016094 and is currently supported by the Office of Research Infrastructure Programs/OD R24OD010928, the Cat Health Network grant D12FE-508, and the Center for Companion Animal Health, School of Veterinary Medicine, University of California, Davis. Richard Malik is supported by the Valentine Charlton Bequest from the University of Sydney. Support for the development of the Illumina Infinium Feline 63K iSelect DNA array was provided by the Morris Animal Foundation (http://www.morrisanimalfoundation.org) via a donation from Hill’s Pet Food, Inc. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: lalyons@ucdavis.edu Introduction Potassium is the most abundant cation in mammals [1,2]. The resting membrane potential of cells is affected by the relationship between intracellular and extracellular potassium concentrations and the resting potassium conductance [3]. Since the extracellular potassium greatly affects the tendency of cells to fire action potentials, potassium plays a crucial role in the function of nervous tissue and muscle (skeletal, cardiac and smooth) throughout the body [1,2], implying perturbations can be debilitating or even life- threatening. To maintain ideal body homeostasis, potassium excretion and dietary intake must be balanced [4–6]. Abnormal- ities of potassium homeostasis can occur as a primary condition, or as a secondary disorder [7–10]. Inherited hypokalemia has been discovered in a variety of mammals by genetic studies of individuals and families affected by clinical disease. A classic syndrome of myopathic weakness, hyperkalemic periodic paralysis (HYPP), has been defined genetically in humans [11–14] and horses [15–18]. Genetic studies have shown that in humans, HYPP is attributable to a channelopathy associated with abnormal sodium conductance, usually inherited as an autosomal dominant trait. Primary hypokalemic disorders have been documented in humans, manifesting as episodic weakness associated with low serum potassium [19]. Feline hypokalaemic periodic paralysis or Burmese hypokalaemic periodic polymyopathy (BHP) has been recognized since the seminal cases described by Blaxter and colleagues [20]. The disease is characterized by muscle weakness associated with intermittent hypokalemia [21]. Genetic studies suggest an autosomal recessive condition in Burmese cats [20]. Blaxter [20] provided a full description of the condition in the Burmese cat breed of the United Kingdom, Jones and collaborators recorded similar findings within Burmese cats from New Zealand [22], while Mason and Lantinga documented the condition in cats in PLOS ONE | www.plosone.org 1 December 2012 | Volume 7 | Issue 12 | e53173 * Aristaless-Like Homeobox protein 1 (ALX1) variant associated with craniofacial structure and frontonasal dysplasia in Burmese cats Leslie A. Lyons a,f,n , Carolyn A. Erdman b,f , Robert A. Grahn c,f , Michael J. Hamilton d,f , Michael J. Carter e,f , Christopher R. Helps g , Hasan Alhaddad h , Barbara Gandolfi a,f a Department of Veterinary Medicine & Surgery, College of Veterinary Medicine, University of Missouri-Columbia, Columbia, MO 65211, USA b Department of Psychiatry, University of California-San Francisco, San Francisco, CA 94143, USA c Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA 96516, USA d Department of Cell Biology and Neuroscience, Institute for Integrative Genome Biology, Center for Disease Vector Research, University of California-Riv- erside, Riverside, CA 92521, USA e MDxHealth Inc, 15279 Alton Parkway, Suite #100, Irvine, CA 92618, USA f Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA 95776, USA g Langford Veterinary Services, University of Bristol, Bristol BS40 5DU, UK h College of Science, Kuwait University, Safat, Kuwait a r t i c l e i n f o Article history: Received 2 October 2015 Received in revised form 3 November 2015 Accepted 20 November 2015 Keywords: Cartilage homeo protein 1 CART1 Domestic cat Facial development Frontonasal dysplasia FND Felis silvestris catus a b s t r a c t Frontonasal dysplasia (FND) can have severe presentations that are medically and socially debilitating. Several genes are implicated in FND conditions, including Aristaless-Like Homeobox 1 (ALX1), which is associated with FND3. Breeds of cats are selected and bred for extremes in craniofacial morphologies. In particular, a lineage of Burmese cats with severe brachycephyla is extremely popular and is termed Contemporary Burmese. Genetic studies demonstrated that the brachycephyla of the Contemporary Burmese is a simple co-dominant trait, however, the homozygous cats have a severe craniofacial defect that is incompatible with life. The craniofacial defect of the Burmese was genetically analyzed over a 20 year period, using various genetic analysis techniques. Family-based linkage analysis localized the trait to cat chromosome B4. Genome-wide association studies and other genetic analyses of SNP data refined a critical region. Sequence analysis identified a 12 bp in frame deletion in ALX1, c.496delCTCTCAGGACTG, which is 100% concordant with the craniofacial defect and not found in cats not related to the Con- temporary Burmese. & 2015 Published by Elsevier Inc. 1. Introduction Frontonasal dysplasia (FND) or median cleft syndrome is a heterogeneous group of disorders that describes an array of ab- normalities affecting development of the maxilla-facial structures and the skull. The prevalence of FND is unknown and is considered a rare or “orphan” disease (ORPHA no.: ORPHA250), however af- fected children can have severe presentations that are life-long medically and socially debilitating. Three genes have been im- plicated in FND conditions. Aristaless-Like Homeobox 1 (ALX1) (OMIM:601527) is associated with FND3, which was defined in three Turkish sibs of consanguineous parents (Uz et al., 2010). ALX1 is also known as Cartilage homeoprotein-1 (CART1) (Zhao et al., 1993), which has been demonstrated to cause neural tube defects in mice (Zhao et al., 1996), presenting as acrania and meroanencephaly in mice. Domesticated animals are often selected for craniofacial var- iants that become breed defining traits. Conditions that would be considered abnormalities or severe craniofacial defects in humans are desired phenotypes in cats and dogs, thus companion animals are excellent models for human facial development due to their popularity. Many dog and cat breeds are bred for brachycephaly, which is assumed to be preferred due to its neotenic effect on the animal's face. In dogs, the definition of brachycephaly has been quantified by morphological measurements (Huber and Lups, 1968; Koch et al., 2012; Regodon et al., 1991; Schmidt et al., 2011) and two genes have been implicated for affecting head type (Haworth et al., 2001; Hunemeier et al., 2009; Schoenebeck et al., 2012). The health concerns associated with canine brachycephaly have come under strong veterinary and public scrutiny (Kruijsen and Wayop, 2011; Oechtering et al., 2010; Roberts et al., 2010), Contents lists available at ScienceDirect journal homepage: www.elsevier.com/locate/developmentalbiology Developmental Biology n Correspondence to: Department of Veterinary Medicine & Surgery, College of Veterinary Medicine, University of Missouri-Columbia, E109 Vet Med Building, Developmental Biology ∎ (∎∎∎∎) ∎∎∎–∎∎∎ SHORT COMMUNICATION COLQ variant associated with Devon Rex and Sphynx feline hereditary myopathy Barbara Gandolfi1 , Robert A. Grahn2 , Erica K. Creighton1 , D. Colette Williams3 , Peter J. Dickinson4 , Beverly K. Sturges4 , Ling T. Guo4 , G. Diane Shelton5 , Peter A. J. Leegwater6 , Maria Longeri7 , Richard Malik8 and Leslie A. Lyons1 1 Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri – Columbia, Columbia, MO 65211, USA. 2 Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California – Davis, Davis, CA 95616, USA. 3 The William R. Pritchard Veterinary Medical Teaching Hospital, School of Veterinary Medicine, University of California – Davis, Davis, CA 95616, USA. 4 Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California – Davis, Davis, CA 95616, USA. 5 Department of Pathology, University of California – San Diego, La Jolla, CA 92093, USA. 6 Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, 3508 TD, Utrecht, The Netherlands. 7 Dipartimento di Scienze Veterinarie e Sanita Pubblica, University of Milan, Milan, Italy. 8 Centre for Veterinary Education, University of Sydney, Sydney, NSW 2006, Australia. Summary Some Devon Rex and Sphynx cats have a variably progressive myopathy characterized by appendicular and axial muscle weakness, megaesophagus, pharyngeal weakness and fatigability with exercise. Muscle biopsies from affected cats demonstrated variable pathological changes ranging from dystrophic features to minimal abnormalities. Affected cats have exacerbation of weakness following anticholinesterase dosing, a clue that there is an underlying congenital myasthenic syndrome (CMS). A genome-wide association study and whole-genome sequencing suggested a causal variant for this entity was a c.1190GA variant causing a cysteine to tyrosine substitution (p.Cys397Tyr) within the C-terminal domain of collagen-like tail subunit (single strand of homotrimer) of asymmetric acetyl- cholinesterase (COLQ). Alpha-dystroglycan expression, which is associated with COLQ anchorage at the motor end-plate, has been shown to be deficient in affected cats. Eighteen affected cats were identified by genotyping, including cats from the original clinical descriptions in 1993 and subsequent publications. Eight Devon Rex and one Sphynx not associated with the study were identified as carriers, suggesting an allele frequency of ~2.0% in Devon Rex. Over 350 tested cats from other breeds did not have the variant. Characteristic clinical features and variant presence in all affected cats suggest a model for COLQ CMS. The association between the COLQ variant and this CMS affords clinicians the opportunity to confirm diagnosis via genetic testing and permits owners and breeders to doi: 10.1111/age.12350 Genetic Susceptibility to Feline Infectious Peritonitis in Birman Cats Lyudmila Golovkoa, Leslie A. Lyonsb, Hongwei Liua, Anne Sorensenc, Suzanne Wehnertc, and Niels C. Pedersena,1 aCenter for Companion Animal Health, School of Veterinary Medicine, University of California, One Shields Avenue, Davis, CA 95616, USA bDepartment of Population Health and Reproduction, University of California, One Shields Avenue, Davis, CA 95616, USA cFasanvejens Dyreklinik, Sondre Fasanvej 93, DK 2500 Valby Denmark NIH Public Access Author Manuscript Virus Res. Author manuscript; available in PMC 2015 February 27. Published in final edited form as: Virus Res. 2013 July ; 175(1): 58–63. doi:10.1016/j.virusres.2013.04.006. NIH-PAAuthorManuscriptNI
  31. 31. A splice variant in KRT71 is associated with curly coat phenotype of Selkirk Rex cats Barbara Gandolfi1 , Hasan Alhaddad1 , Shannon E. K. Joslin1 , Razib Khan1 , Serina Filler2 , Gottfried Brem2 Leslie A. Lyons1 1 Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, Davis, CA USA, 2 Institute of Animal Breeding and Genetics, Department for Biomedical Sciences, University of Veterinary Medicine - Vienna, Vienna, Austria. One of the salient features of the domestic cat is the aesthetics of its fur. The Selkirk Rex breed is defined by an autosomal dominant woolly rexoid hair (ADWH) abnormality that is characterized by tightly curled hair shafts. A genome-wide case – control association study was conducted using 9 curly coated Selkirk Rex and 29 controls, including straight-coated Selkirk Rex, British Shorthair and Persian, to localize the Selkirk autosomal dominant rexoid locus (SADRE). Although the control cats were from different breed lineages, they share recent breeding histories and were validated as controls by Bayesian clustering, multi-dimensional scaling and genomic inflation. A significant association was found on cat chromosome B4 (Praw 5 2.87 3 10211 ), and a unique haplotype spanning ,600 Kb was found in all the curly coated cats. Direct sequencing of four candidate genes revealed a splice site variant within the KRT71 gene associated with the hair abnormality in Selkirk Rex. B ody homeostasis and tissue integration are supported by the hair, a highly keratinized tissue produced in the hair follicle (HF). Hair formation in mammalian HFs occurs during embryogenesis through a series of reciprocal interactions between skin epithelial and underlying dermal cells1,2 . The HF undergoes dynamic cell kinetics composed of the anagen (active growth) phase, the catagen (transition) phase, and the telogen (resting) phase3 . Among the skin appendages, the HF has a highly complex structure with eight distinct cell layers, where hundreds of gene products play key roles in hair cycle and maintenance. The hair shaft is sur- rounded and supported by the inner root sheath, the companion layer, and the outer root sheath4 . The formation of a rigid structure during the HF differentiation is due to keratin proteins that are abundantly and differentially expressed2,4,5 . A mammal’s pelage is generally one of its most noticeable attributes and is aesthetically pleasing. In cats, coat color and pelage types are often selected as a specific trait to develop a breed. The coat of a normal cat consists three hair types: long and straight guard hairs of uniform diameter, thinner awn hairs, and the fine undulating down hairs of uniform thickness6 . Rexoid (curly / woolly) pelage is an easily recognized trans-species anomaly; detailed studies in various mammalian species, including mice7,8 , chicken9 , rat10 , dog11 and human12–15 , have identified causative genes and mutations. Nine rexoid-type pelage phenotypes are known within the domestic cat16–20 and recently, significant advances have been made toward the identification of these feline hair abnor- malities. One study revealed two alleles (KRT71re and KRT71hr ) within KRT71, a crucial gene for keratinization in the HF, which are responsible for recessive hypotricosis Hairless (Hr, hr) locus of the Sphynx breed and the Rex hair locus (Re, re) of the curly coated Devon Rex breed19 . A second rexoid locus (R, r) with a mutation within P2RY5 is responsible for the autosomal recessive woolly hair in the Cornish Rex breed (Gandolfi 2013, in press). For each of these autosomal recessive rexoid / woolly hair conditions, the identified mutations are responsible for a major change in the hair follicle, altering hair formation. Several dominant rexoid / woolly hair conditions define other breeds, such as Selkirk Rex, LaPerm and American Wirehair, and these mutations await identifica- tion and characterization. OPEN SUBJECT AREAS: GENOME-WIDE ASSOCIATION STUDIES RNA SPLICING SKIN MODELS HAPLOTYPES Received 17 December 2012 Accepted 22 May 2013 Published 17 June 2013 Correspondence and requests for materials should be addressed to B.G. (bgandolfi@ ucdavis.edu) GWAS ARTICLE IN PRESSG Model VETIMM-9250; No. of Pages 8 Veterinary Immunology and Immunopathology xxx (2014) xxx–xxx Contents lists available at ScienceDirect Veterinary Immunology and Immunopathology journal homepage: www.elsevier.com/locate/vetimm Research paper The influence of age and genetics on natural resistance to experimentally induced feline infectious peritonitis Niels C. Pedersena,∗ , Hongwei Liua , Barbara Gandolfib,c , Leslie A. Lyonsb,c a Center for Companion Animal Health, School of Veterinary Medicine, University of California—Davis, One Shields Avenue, Davis, CA 95616, USA b Department of Population Health Reproduction, School of Veterinary Medicine, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA c Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, Columbia, MO 65211, USA a r t i c l e i n f o Article history: Received 20 May 2014 Received in revised form 12 August 2014 Accepted 8 September 2014 Keywords: Feline infectious peritonitis Experimental Natural immunity Age resistance Genetic resistance GWAS a b s t r a c t Naturally occurring feline infectious peritonitis (FIP) is usually fatal, giving the impression that immunity to the FIP virus (FIPV) is extremely poor. This impression may be incor- rect, because not all cats experimentally exposed to FIPV develop FIP. There is also a belief that the incidence of FIP may be affected by a number of host, virus, and environmental cofactors. However, the contribution of these cofactors to immunity and disease incidence has not been determined. The present study followed 111 random-bred specific pathogen free (SPF) cats that were obtained from a single research breeding colony and experimen- tally infected with FIPV. The cats were from several studies conducted over the past 5 years, and as a result, some of them had prior exposure to feline enteric coronavirus (FECV) or avirulent FIPVs. The cats were housed under optimized conditions of nutrition, husbandry, and quarantine to eliminate most of the cofactors implicated in FIPV infection outcome and were uniformly challenge exposed to the same field strain of serotype 1 FIPV. Forty of the 111 (36%) cats survived their initial challenge exposure to a Type I cat-passaged field strains of FIPV. Six of these 40 survivors succumbed to FIP to a second or third challenge exposure, suggesting that immunity was not always sustained. Exposure to non-FIP-inducing feline coronaviruses prior to challenge with virulent FIPV did not significantly affect FIP incidence but did accelerate the disease course in some cats. There were no significant differences in FIP incidence between males and females, but resistance increased significantly between Genome-wide association and linkage analyses localize a progressive retinal atrophy locus in Persian cats Hasan Alhaddad • Barbara Gandolfi • Robert A. Grahn • Hyung-Chul Rah • Carlyn B. Peterson • David J. Maggs • Kathryn L. Good • Niels C. Pedersen • Leslie A. Lyons Received: 19 February 2014 / Accepted: 3 April 2014 / Published online: 29 April 2014 Ó The Author(s) 2014. This article is published with open access at Springerlink.com Abstract Hereditary eye diseases of animals serve as excellent models of human ocular disorders and assist in the development of gene and drug therapies for inherited consistently supported significant association within the same region on chromosome E1, which is homologous to human chromosome 17. Using haplotype analysis, a Mamm Genome (2014) 25:354–362 DOI 10.1007/s00335-014-9517-z
  32. 32. To the Root of the Curl: A Signature of a Recent Selective Sweep Identifies a Mutation That Defines the Cornish Rex Cat Breed Barbara Gandolfi1 *, Hasan Alhaddad1 , Verena K. Affolter2 , Jeffrey Brockman3 , Jens Haggstrom4 , Shannon E. K. Joslin1 , Amanda L. Koehne2 , James C. Mullikin5 , Catherine A. Outerbridge6 , Wesley C. Warren7 , Leslie A. Lyons1 1 Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, Davis, California, United States of America, 2 Department of Pathology, Microbiology, Immunology, School of Veterinary Medicine, University of California - Davis, Davis, California, United States of America, 3 Hill’s Pet Nutrition Center, Topeka, Kansas, United States of America, 4 Department of Clinical Sciences, Faculty of Veterinary Medicine and Animal Science, Swedish University of Agricultural Sciences, Uppsala, Sweden, 5 Comparative Genomics Unit, Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America, 6 Department of Veterinary Medicine Epidemiology, School of Veterinary Medicine, University of California - Davis, Davis, California, United States of America, 7 The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America Abstract The cat (Felis silvestris catus) shows significant variation in pelage, morphological, and behavioral phenotypes amongst its over 40 domesticated breeds. The majority of the breed specific phenotypic presentations originated through artificial selection, especially on desired novel phenotypic characteristics that arose only a few hundred years ago. Variations in coat texture and color of hair often delineate breeds amongst domestic animals. Although the genetic basis of several feline coat Selection • Breed defining traits (mutations fixed) • No controls (can’t perform case-control GWAS)! • Investigate the breed history to identify breed defining mutation(s).
  33. 33. Beyond traits/diseases 0 1 2 3 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 %Bengalness 0255075100 ALC LxD BEN ACURL 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: 1)  Department of Biological Science, Kuwait University, Kuwait 2)  College of Veterinary Medicine, University of Missouri-Columbia, Columbia, MO 3)  Department of Population Health Reproduction, University of California - Davis, Davis, CA Degree of Bengalness: A measure of the measure of genomic contribution of Asian Leopard Cats into Bengal breed cats Mona Abdi1, H. Alhaddad1, B. Gandolfi2 R. Grahn3, and L. A. Lyons2 Dataset Analysis: The idea Significance •  The Bengal breed cats result from hybridizing domestic cats (DOM) and Asian Leopard Cats (ALC). •  First generation hybrids can be further crossed to domestic cats and still be considered Bengal cats as long as phenotypic and behavioral characteristics retained (see cat below). •  The ALC genomic contribution into registered Bengal cats is usually unknown and likely variable. •  Significance of the study: 1.  Develop a panel of diagnostic markers to measure ALC genomic contribution in Bengal cats (degree of Bengalness). 2.  The panel can be used to study the genetics of the Asian Leopard cat and the ALC-DOM introgression zones in the wild. Dataset: •  A total of 2161 cats (from 48 breeds/populations) genotyped using the 63K Feline SNP array were used. •  ALC (N = 9) and domestic cats (N = 1765). •  Calculate the allele frequency for each marker in each group independently. •  Select the markers that are fixed with allele 1 (A1) in ALC and absent in domestic cats or have a minor allele frequency 0.05. •  Evaluate the positions of the selected markers. •  Select a subset of the identified markers with near uniform inter-marker distances. Objective 1: Identify diagnostic markers that are fixed for different alleles in the two groups (ALC DOM) 1.  674 markers were identified as diagnostic markers and they were distributed in all 19 cat chromosomes (Fig. 1a). 2.  To avoid markers being in linkage disequilibrium, 287 were selected with an inter-marker distance ~ 5 Mb (Fig. 1b). Fig.1: Distribution of ALC specific markers along cat chromosomes. (a) Relative positions of all markers identified. Many markers are close to one another and may be in linkage disequilibrium. (b) Relative position of a subset of markers from (a) where markers are ~ 5Mb apart. 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 a. SNP Relative Position (Mb)b. 0 25 50 75 100 125 150 175 200 225 250 Objective 2: Estimate the genomic contribution of ALC in: (1) known pedigree, (2) Bengal breed, (3) Other cat breed Dataset Analysis: •  Diagnostic panel (All: 287 markers, Auto: 262 markers). •  ALC-DOM pedigree (N = 98), random Bengal cat (N = 98), and 33 cat breeds (N = 1452). •  Calculate % of ALC alleles (% bengalness) in each individual using autosomal markers only. •  Using known pedigree samples, estimate range of % bengalness and validate the estimates using pedigree information. Fig. 2: Genomic contribution of ALC. (a). Known pedigree crosses of ALC-DOM. LxD: first generation hybrid. BxL: backcross to ALC. BxD: backcross to DOM. BEN: Bengal cat unknown pedigree (b). Percent bengalness in known pedigree, random bengal cats, and other cat breeds. ALC DOM LxDBxL BxD BENa. b. Findings: 1.  Known ALC-DOM pedigree (Fig. 2a) provides information about theoretical % bengalness. In pedigree samples, theoretical and observed are similar (Fig. 2b, Table 1). 2.  Random Bengal cats on average have ~ 7% benglness whereas other cat breeds, combined, exhibit ~ 1% with some variations (Table 1). 3.  Proportion of ALC into Bengal cats is unmatched by any of the other breeds with the exception of Turkish Van (Fig. 2b). 4.  The relatively low % bengalness of random Bengal cats indicates multiple crosses to DOM or breeding between Bengal cats. 5.  Using 262 (autosomal) diagnostic panel is sufficient to identify Bengal cats and estimate ALC contribution. Groups Theoretical Mean (Observed) s.d.(Observed) ALC 100 100 0 BxL 75 73 10.75 LxD 50 47 11.5 BxD 25 24.5 3.5 BEN unknown 7 2 DOM ~ 0 1.25 0.5 Table 1: Theoretical and observed percent bengalness in different cat groups. Objective 3: Estimate the number of generations that gives a particular % bengalness Dataset Analysis: •  ALC-DOM pedigree (N = 98), random Bengal cat (N = 98). •  Use estimated % bengalness in each group. •  Determine the number of generations crossed to DOM that results into random Bengal cats. •  Use the theoretical relationship between % bengalness and number of generations crossed to domestic depicted as: % Bengalness = 100 x (½) # generations •  Infer theoretical number of generations since the initial hybridization for each Bengal cat . Findings: 1.  First generation hybrids (LxD) exhibit small variation in % bengalness while backcross to ALC (BxL) and DOM (BxD) show significant variation between individuals (Fig. 3). 2.  The % bengalness of random Bengal cats places them in the range of 3-5 generations of theoretical hybridization with concentration around generation 4 (6.75%) (Fig.3). 3.  Variation in % bengalness can be explained by breeding between dissimilar (ALC-DOM) and similar (BEN-BEN) individuals. 4.  The small variation of % bengalness among Bengal cats is a sign of state equilibrium that results from breeding between Bengal cats and no or infrequent introduction of ALC or DOM alleles into the breed. Fig. 3: Percent bengalness as function of generation number. Poster number P0501
  34. 34. Conclusion • SNP information update • Ready to use comprehensive dataset • Genome-wide analysis of cat breeds • GWAS-Selection-Beyond
  35. 35. Questions?
  36. 36. Disclaimer Figures, photos, and graphs 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

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