Successfully reported this slideshow.
We use your LinkedIn profile and activity data to personalize ads and to show you more relevant ads. You can change your ad preferences anytime.
The genomic landscape of
selection in domestic cat breeds
Hasan Alhaddad
PAG 2019
Study Objectives
• Identify signatures of selection for individual cat
breeds using multiple methods.
• Compare the candid...
Domestication
Domestication and breed formation
Personal Synthesis
A. Ecological domestication
B. Selection from standing variation in R...
Cat breeds
Selected traits
Face & Ears
Hair-length & Texture
Legs & Tail
Color & Pattern
Data
Samples
2162 cat samples
41 cat breeds
Wild cats
Pedigree cats
Markers
~63K SNPs
Autosomal SNPs
X-Chr SNPs
UN-Chr SNPs
App...
Final Dataset
Samples
90% genotyping rate
Recognized breeds
Sample size ≥ 5
Unrelated samples
Markers
90% genotyping rate
...
Sample size
Mean (di) per 500Kb
Frequency
-40 -20 0 20 40 60 80
02006001000
Bengal1
Bengal2
-40 -20 0 20 40 60 80
-40-2002...
-0.04 -0.02 0.00 0.02 0.04 0.06 0.08
-0.15-0.10-0.050.000.05
PC1 (28.9%)
PC2(9.5%)
a.
-0.045 -0.035 -0.025 -0.015
-0.04-0....
-0.04 -0.02 0.00 0.02 0.04 0.06 0.08
-0.15-0.10-0.050.000.05
PC1
PC2
Birman
a.
-0.04 -0.02 0.00 0.02 0.04 0.06 0.08-0.15-0...
Methods
• Frequency (Fst, di).
• Haplotype (iHS- integrated haplotype homozygosity
score).
• Window: a window of 500Kb size with a...
1 4 9 14 19 24 29 33 37 41 45 49 53 57 63
2Mb
020406080
1 3 5 7 9 12 15 18 21 24 27 30 33 39
1Mb
050150
1 3 5 7 9 11 13 15...
Breed specific analysis
To the Root of the Curl: A Signature of a Recent Selective
Sweep Identifies a Mutation That Defines the Cornish
Rex Cat Br...
LaPerm breed
Chr.B1
0.00.10.20.30.40.5
Fst
-20020406080
di
01234
Chromosome
iHS
A1
A2
A3
B1
B2
B3
B4
C1
C2
D1
D2
D3
D4
E1
...
0.00.10.20.30.40.5
Fst
-20020406080
di
01234
Chromosome
iHS
A1
A2
A3
B1
B2
B3
B4
C1
C2
D1
D2
D3
D4
E1
E2
E3
F1
F2
Egyptian...
General Summary
NumberofSignificantRegions
020406080100
A1 A2 A3 B1 B2 B3 B4 C1 C2 D1 D2 D3 D4 E1 E2 E3 F1 F2
Chromosomes
Fst-based Haplot...
0510152025
Persian1
Persian2
BritishShorthair
SelkirkRex
ScottishFold1
ScottishFold2
MaineCoon
NorwegianForestCat
American...
0 20 40 60 80
Persian1
Persian2
BritishShorthair
SelkirkRex
ScottishFold1
ScottishFold2
MaineCoon
NorwegianForestCat
Ameri...
Breed comparison
(selected regions)
0 153
Siamese
Korat
Burmese2
Burmese1
Oriental
KhaoManee
Birman2
Birman1
Bombay
Peterbald
Ocicat
LaPerm
JapaneseBobtail
Ru...
0 99
Siamese
Korat
Burmese2
Burmese1
Oriental
KhaoManee
Birman2
Birman1
Bombay
Peterbald
Ocicat
LaPerm
JapaneseBobtail
Rus...
Peterbald
Ocicat
LaPerm
JapaneseBobtail
RussianBlue
CornishRex
Ragdoll2
Ragdoll1
Bengal2
Bengal1
TurkishVan
AmericanCurl
D...
0 143
Siamese
Korat
Burmese2
Burmese1
Oriental
KhaoManee
Birman2
Birman1
Bombay
Peterbald
Ocicat
LaPerm
JapaneseBobtail
Ru...
General view of selection
0 241Chromosome Length (Mb)
A1
A2
A3
B1
B2
B3
B4
C1
C2
D1
D2
D3
D4
E1
E2
E3
F1
F2
Fst-based
0 241Chromosome Length (Mb)
A1...
41/789
273
10/275
155
33/744
695
5/169
583
Breeds/Samples
Fst-based Sweeps
0 241Chromosome Length (Mb)
A1
A2
A3
B1
B2
B3
B...
What is next?
Leslie A. Lyons, PhD
Department of Veterinary Medicine and Surgery
Acknowledgment
Mona Abdi, M.Sc.
Department of Biologica...
Disclaimer
Figures, photos, and graphs in my presentations are
collected using google searches. I do not claim to have
per...
Cat signatures of selection
Upcoming SlideShare
Loading in …5
×

Cat signatures of selection

56 views

Published on

This was my presentation at the Plant and Animal Genome Conference 2019 in San Diego. My talk was a presentation of the thesis project of my student Mona Abdi. The focus of the presentation and project was the genomic signatures of selection in the domestic cat breeds.

Published in: Science
  • Be the first to comment

  • Be the first to like this

Cat signatures of selection

  1. 1. The genomic landscape of selection in domestic cat breeds Hasan Alhaddad PAG 2019
  2. 2. Study Objectives • Identify signatures of selection for individual cat breeds using multiple methods. • Compare the candidate regions under selection between breeds. • Provide an overall view of the genomic landscape of the domestic cat.
  3. 3. Domestication
  4. 4. Domestication and breed formation Personal Synthesis A. Ecological domestication B. Selection from standing variation in RB C. Selection from standing variation in breed D. Breeds from de novo mutation E. Hybridizing two (more) breeds F. Interspecies hybridization
  5. 5. Cat breeds
  6. 6. Selected traits
  7. 7. Face & Ears Hair-length & Texture Legs & Tail Color & Pattern
  8. 8. Data
  9. 9. Samples 2162 cat samples 41 cat breeds Wild cats Pedigree cats Markers ~63K SNPs Autosomal SNPs X-Chr SNPs UN-Chr SNPs Applications and efficiencies of the first cat 63K DNA array BarbaraGandolfi1 , HasanAlhaddad2 , MonaAbdi2 , Leslie H. Bach3,4 , Erica K.Creighton1 , BrianW. Davis 5 ,Jared E. Decker 6 , Nicholas H. Dodman7 ,JenniferC.Grahn3,8 , RobertA. Grahn3,8 , Bianca Haase9 ,Jens Haggstrom10 , MichaelJ. Hamilton3,11 ,Christopher R. Helps12 , Jennifer D. Kurushima3,13 , Hannes Lohi14 , Maria Longeri15 , Richard Malik16 , Kathryn M. Meurs17 , MichaelJ. Montague 18 ,JamesC. Mullikin 19 ,WilliamJ. Murphy5 ,Sara M. Nilson6 , NielsC. Pedersen20 ,Carlyn B. Peterson3 ,Clare Rusbridge21 , RashidSaif22 ,G. DianeShelton23 , WesleyC.Warren24 , MuhammadWasim25 & LeslieA. Lyons1 The development of high throughput SNP genotyping technologies has improved the genetic dissection of simple and complex traits in many species including cats.The properties of feline 62,897 SNPs Illumina Infinium iSelect DNA array are described using a dataset of over 2,000 feline samples, the most extensive to date, representing 41 cat breeds, a random bred population, and four wild felid species. Accuracy and efficiency of the array’s genotypes and its utility in performing population-based analyses were evaluated.Average marker distance across the array was 37,741 Kb, and across the dataset, only 1% (625) of the markers exhibited poor genotyping and only 0.35% (221) showed Mendelian errors. Marker polymorphism varied across cat breeds and the average minor allele frequency (MAF) of all markers across domestic cats was 0.21. Population structure analysis confirmed aWestern to Eastern structural continuum of cat breeds.Genome-wide linkage disequilibrium ranged from 50–1,500 Kb for domestic cats and 750 Kb for European wildcats (Felis silvestris silvestris).Array use in trait association mapping was investigated under different modes of inheritance, selection and population sizes.The efficient array design and cat genotype dataset continues to advance the understanding of cat breeds and will support monogenic health studies across feline breeds and populations. 1 Department ofVeterinary Medicine andSurgery,College ofVeterinary Medicine,University of Missouri -Columbia, Columbia, MO, USA. 2 Department of Biological Sciences, Kuwait University, Safat, Kuwait. 3 Department of Population Health and Reproduction,School ofVeterinary Medicine,University ofCalifornia – Davis, Davis,CA,USA. 4 University ofSan Francisco,San Francisco,CA,USA. 5 Department ofVeterinary Integrative Biosciences,TexasA&M University,CollegeStation,TX,USA. 6 Division ofAnimalSciences,University of Missouri -Columbia,Columbia, MO, USA. 7 Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA, USA. 8 Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California - Davis, Davis, CA, USA. 9 Sydney School of VeterinaryScience,University ofSydney,Sydney,Australia. 10 Department ofClinicalSciences,SwedishUniversity of AgriculturalSciences,Uppsala,Sweden. 11 Department of Biochemistry,University ofCalifornia – Riverside, Riverside, CA, USA. 12 LangfordVets, University of Bristol, Bristol, United Kingdom. 13 FoothillCollege, LosAltos Hills,CA, USA. 14 Department of Veterinary Biosciences, Research Programs Unit, Molecular Neurology, University of Helsinki, andThe Folkhälsan Institute of Genetics, Helsinki, Finland. 15 Department ofVeterinary Medicine, Università degli Studi di Milano, Milan, Italy. 16 Centre forVeterinary Education, University of Sydney, New South Wales, Australia. 17 Department ofClinicalSciences,College ofVeterinary Medicine, NorthCarolinaStateUniversity, Raleigh, NC,USA. 18 Department of Neuroscience, Parelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. 19 NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD,USA. 20 Center forCompanionAnimal Health,School ofVeterinary Medicine,University ofCalifornia - Davis, Davis,CA,USA. 21 School ofVeterinary Medicine, Faculty of Health and MedicalSciences,University ofSurrey, Guildford,Surrey,United Kingdom. 22 Institute of Biotechnology,Gulab Devi EducationalComplex, Lahore, Pakistan. 23 Department of Pathology, University of California, San Diego, La Jolla, CA, USA. 24 McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA. 25 Institute of Biochemistry and Biotechnology, University ofVeterinary and Animal Sciences, Lahore, Pakistan. Barbara Gandolfi and Hasan Alhaddad contributed Received: 17 October 2017 Accepted: 16 April 2018 Published: xx xx xxxx OPEN Correction: Author Correction Original Dataset
  10. 10. Final Dataset Samples 90% genotyping rate Recognized breeds Sample size ≥ 5 Unrelated samples Markers 90% genotyping rate Autosomal SNPs MAF ≥ 0.05 789 cat samples 34 breeds Sample size (5-25) 51813 autosomal SNPs
  11. 11. Sample size Mean (di) per 500Kb Frequency -40 -20 0 20 40 60 80 02006001000 Bengal1 Bengal2 -40 -20 0 20 40 60 80 -40-20020406080 Mean (di) Bengal (1) Mean(di)Bengal(2) -40 -20 0 20 40 60 80 -40-20020406080 Mean (di) Bengal Mean(di)non-Bengal Mean (Fst) per 500Kb Frequency 0.0 0.1 0.2 0.3 0.4 0.5 02006001000 Bengal1 Bengal2 0.0 0.1 0.2 0.3 0.4 0.5 0.00.10.20.30.40.5 Mean (Fst) Bengal (1) Mean(Fst)Bengal(2) 0.0 0.1 0.2 0.3 0.4 0.5 0.00.10.20.30.40.5 Mean (Fst) Bengal Mean(Fst)non-Bengal
  12. 12. -0.04 -0.02 0.00 0.02 0.04 0.06 0.08 -0.15-0.10-0.050.000.05 PC1 (28.9%) PC2(9.5%) a. -0.045 -0.035 -0.025 -0.015 -0.04-0.03-0.02-0.010.000.01 BSH MCOON MANX NFC PER SFOLD SREX WIR CHR LYK b. -0.02 -0.01 0.00 0.01 0.02 -0.04-0.020.000.020.04 ABY BEN DREX EGY JBOB PERM OCI RAG RBLUE SPH Van ACURL CREX SOM c. 0.03 0.04 0.05 0.06 0.07 0.08 -0.15-0.10-0.050.000.05 BIR BUR MANEE KOR ORI PBALD SIA d. Group 1 Western Breeds Group 2 Middle Breeds Group 3 Eastern Breeds
  13. 13. -0.04 -0.02 0.00 0.02 0.04 0.06 0.08 -0.15-0.10-0.050.000.05 PC1 PC2 Birman a. -0.04 -0.02 0.00 0.02 0.04 0.06 0.08-0.15-0.10-0.050.000.05 PC1 PC3 Bengal b. -0.04 -0.02 0.00 0.02 0.04 0.06 0.08 -0.10-0.050.000.05 PC1 PC4 c. -0.04 -0.02 0.00 0.02 0.04 0.06 0.08 -0.15-0.10-0.050.000.05 PC2 PC3 Bengal d. -0.04 -0.02 0.00 0.02 0.04 0.06 0.08 -0.06-0.04-0.020.000.020.04 PC2 PC4 Bengal Birman e. -0.15 -0.10 -0.05 0.00 0.05 -0.06-0.04-0.020.000.020.04 PC3 PC4 Bengal f. Group 1 Western Breeds Group 2 Middle Breeds Group 3 Eastern Breeds
  14. 14. Methods
  15. 15. • Frequency (Fst, di). • Haplotype (iHS- integrated haplotype homozygosity score). • Window: a window of 500Kb size with at least 5 SNPs. • Threshold: significance (0.01) of the empirical distribution of the three statistics. • Candidate Regions :Consecutive significant windows (two or more).
  16. 16. 1 4 9 14 19 24 29 33 37 41 45 49 53 57 63 2Mb 020406080 1 3 5 7 9 12 15 18 21 24 27 30 33 39 1Mb 050150 1 3 5 7 9 11 13 15 17 19 22 31 41 0.5 Mb 0200500 1 2 3 4 5 6 7 8 9 10 12 14 18 23 0.25 Mb 05001500 0.00.10.20.30.40.50.6 Non-overlap Fst 0.00.10.20.30.40.50.6 Partial overlap Fst 0.00.20.40.6 Total overlap Fst A1 A2 A3 B1 B2 B3 B4 C1 C2 D1 D2 D3 D4 E1 E2 E3 F1 F2
  17. 17. Breed specific analysis
  18. 18. 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 colors and hair lengths are characterized, less is known about the genes influencing variation in coat growth and texture, especially rexoid – curly coated types. Cornish Rex is a cat breed defined by a fixed recessive curly coat trait. Genome-wide analyses for selection (di, Tajima’s D and nucleotide diversity) were performed in the Cornish Rex breed and in 11 phenotypically diverse breeds and two random bred populations. Approximately 63K SNPs were used in the analysis that aimed to localize the locus controlling the rexoid hair texture. A region with a strong signature of recent selective sweep was identified in the Cornish Rex breed on chromosome A1, as well as a consensus block of homozygosity that spans approximately 3 Mb. Inspection of the region for candidate genes led to the identification of the lysophosphatidic acid receptor 6 (LPAR6). A 4 bp deletion in exon 5, c.250_253_delTTTG, which induces a premature stop codon in the receptor, was identified via Sanger sequencing. The mutation is fixed in Cornish Rex, absent in all straight haired cats analyzed, and is also segregating in the German Rex breed. LPAR6 encodes a G protein-coupled receptor essential for maintaining the structural integrity of the hair shaft; and has mutations resulting in a wooly hair phenotype in humans. Citation: Gandolfi B, Alhaddad H, Affolter VK, Brockman J, Haggstrom J, et al. (2013) To the Root of the Curl: A Signature of a Recent Selective Sweep Identifies a Mutation That Defines the Cornish Rex Cat Breed. PLoS ONE 8(6): e67105. doi:10.1371/journal.pone.0067105 Editor: Arnar Palsson, University of Iceland, Iceland Received March 26, 2013; Accepted May 14, 2013; Published June 27, 2013 Copyright: ß 2013 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 project was supported by the National Center for Research Resources and the Office of Research Infrastructure Programs of the National Institute of Health through Grant Number R24 RR016094, the Winn Feline Foundation (W10-14, W11-041), the Center for Companion Animal Health at University of California Davis (2010-09-F) (http://www.vetmed.ucdavis.edu/ccah/index.cfm), and the George and Phyllis Miller Feline Health Fund of the San Francisco Foundation (2008-36-F). 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: JB works for a private company (Hill’s Pet Food, Inc) that partially sponsored the development of the 63k feline SNP array. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. * E-mail: bgandolfi@ucdavis.edu Introduction Phenotypic traits under strong artificial selection within cat breeds vary from body types, muzzle shape, tail length to aesthetically pleasant traits, such as hair color, length and texture. Hair represents one of the defining characteristic of mammals. Hair provides body temperature regulation, protection from environmental elements, and adaptive advantages of camouflage, as well as often having aesthetic value to humans. The hair follicle has a highly complex structure with eight distinct cell layers, in which hundreds of gene products play a key role in the hair cycle maintenance [1,2]. In the past decade, numerous genes expressed in the hair follicle have been identified and mutations in some of these genes have been shown to underlie hereditary hair diseases in humans and other mammals [3]. Hereditary hair diseases in mammals show diverse hair phenotypes, such as sparse or short hairs (hypotrichosis), excessive or elongated hairs (hypertrichosis), and hair shaft anomalies, creating rexoid/woolly hairs [3–12]. Causative genes for the diseases encode various proteins with different functions, such as structural proteins, transcription factors, and signaling molecules. Mutations within structural proteins, such as epithelial and hair keratins, are often associated with hair disease. To date, mutations in several hair keratin genes underlined two hereditary hair disorders: monilethrix, character- PLOS ONE | www.plosone.org 1 June 2013 | Volume 8 | Issue 6 | e67105 0.00.10.20.30.40.5 Fst -20020406080 di 01234 Chromosome iHS A1 A2 A3 B1 B2 B3 B4 C1 C2 D1 D2 D3 D4 E1 E2 E3 F1 F2 Cornish Rex breed Positive Control Chr.A1 (LPAR6)
  19. 19. LaPerm breed Chr.B1 0.00.10.20.30.40.5 Fst -20020406080 di 01234 Chromosome iHS A1 A2 A3 B1 B2 B3 B4 C1 C2 D1 D2 D3 D4 E1 E2 E3 F1 F2
  20. 20. 0.00.10.20.30.40.5 Fst -20020406080 di 01234 Chromosome iHS A1 A2 A3 B1 B2 B3 B4 C1 C2 D1 D2 D3 D4 E1 E2 E3 F1 F2 Egyptian Mau breed Chr.C2
  21. 21. General Summary
  22. 22. NumberofSignificantRegions 020406080100 A1 A2 A3 B1 B2 B3 B4 C1 C2 D1 D2 D3 D4 E1 E2 E3 F1 F2 Chromosomes Fst-based Haplotype-based
  23. 23. 0510152025 Persian1 Persian2 BritishShorthair SelkirkRex ScottishFold1 ScottishFold2 MaineCoon NorwegianForestCat AmericanWirehair Manx Siberian1 Siberian2 Chartreux Lykoi Munchkins Abyssinian Somali Sphynx EgyptianMau DevonRex AmericanCurl TurkishVan Bengal1 Bengal2 Ragdoll1 Ragdoll2 CornishRex RussianBlue JapaneseBobtail LaPerm Ocicat Peterbald Bombay Birman1 Birman2 KhaoManee Oriental Burmese1 Burmese2 Korat Siamese NumberofSignificantRegions Fst-based Haplotype-based
  24. 24. 0 20 40 60 80 Persian1 Persian2 BritishShorthair SelkirkRex ScottishFold1 ScottishFold2 MaineCoon NorwegianForestCat AmericanWirehair Manx Siberian1 Siberian2 Chartreux Lykoi Munchkins Abyssinian Somali Sphynx EgyptianMau DevonRex AmericanCurl TurkishVan Bengal1 Bengal2 Ragdoll1 Ragdoll2 CornishRex RussianBlue JapaneseBobtail LaPerm Ocicat Peterbald Bombay Birman1 Birman2 KhaoManee Oriental Burmese1 Burmese2 Korat Siamese Size of Significant Regions (Mb) Fst-based Haplotype-based ROH
  25. 25. Breed comparison (selected regions)
  26. 26. 0 153 Siamese Korat Burmese2 Burmese1 Oriental KhaoManee Birman2 Birman1 Bombay Peterbald Ocicat LaPerm JapaneseBobtail RussianBlue CornishRex Ragdoll2 Ragdoll1 Bengal2 Bengal1 TurkishVan AmericanCurl DevonRex EgyptianMau Sphynx Somali Abyssinian Munchkins Lykoi Chartreux Siberian2 Siberian1 Manx AmericanWirehair NorwegianForestCat MaineCoon ScottishFold2 ScottishFold1 SelkirkRex BritishShorthair Persian2 Persian1 Chr. B2 (Mb) Fst-based Haplotype-based ROH (1, 2, 5, 10, 20Mb) 0 153 Siamese Korat Burmese2 Burmese1 Oriental KhaoManee Birman2 Birman1 Bombay Peterbald Ocicat LaPerm JapaneseBobtail RussianBlue CornishRex Ragdoll2 Ragdoll1 Bengal2 Bengal1 TurkishVan AmericanCurl DevonRex EgyptianMau Sphynx Somali Abyssinian Munchkins Lykoi Chartreux Siberian2 Siberian1 Manx AmericanWirehair NorwegianForestCat MaineCoon Chr. B2 (Mb) Persian Family Breeds Size: 15.9 Mb 120 genes SLC35B3, LY86, F13A1, NRN1, RPP40, ECI2, FAM217A, PRPF4B, FAM50B, SLC22A23, PSMG4, TUBB2A, BPHL, RIPK1…. etc
  27. 27. 0 99 Siamese Korat Burmese2 Burmese1 Oriental KhaoManee Birman2 Birman1 Bombay Peterbald Ocicat LaPerm JapaneseBobtail RussianBlue CornishRex Ragdoll2 Ragdoll1 Bengal2 Bengal1 TurkishVan AmericanCurl DevonRex EgyptianMau Sphynx Somali Abyssinian Munchkins Lykoi Chartreux Siberian2 Siberian1 Manx AmericanWirehair NorwegianForestCat MaineCoon ScottishFold2 ScottishFold1 SelkirkRex BritishShorthair Persian2 Persian1 Chr. D2 (Mb) Fst-based Haplotype-based ROH (1, 2, 5, 10, 20Mb) 0 99 Siamese Korat Burmese2 Burmese1 Oriental KhaoManee Birman2 Birman1 Bombay Peterbald Ocicat LaPerm JapaneseBobtail RussianBlue CornishRex Ragdoll2 Ragdoll1 Bengal2 Bengal1 TurkishVan AmericanCurl DevonRex EgyptianMau Sphynx Somali Abyssinian Munchkins Lykoi Chartreux Siberian2 Siberian1 Manx AmericanWirehair NorwegianForestCat MaineCoon ScottishFold2 ScottishFold1 SelkirkRex BritishShorthair Persian2 Persian1 Chr. D2 (Mb) Fst-based Haplotype-based ROH (1, 2, 5, 10, 20Mb) Non-Persian Family Western Breeds One gene ZWINT, codes for ZW10 (Interacting kinetochore protein)
  28. 28. Peterbald Ocicat LaPerm JapaneseBobtail RussianBlue CornishRex Ragdoll2 Ragdoll1 Bengal2 Bengal1 TurkishVan AmericanCurl DevonRex EgyptianMau Sphynx Somali Abyssinian Munchkins Lykoi Chartreux Siberian2 Siberian1 Manx AmericanWirehair NorwegianForestCat MaineCoon ScottishFold2 ScottishFold1 SelkirkRex BritishShorthair Persian2 Persian1 Fst-based Haplotype-based ROH (1, 2, 5, 10, 20Mb) 0 150 Siamese Korat Burmese2 Burmese1 Oriental KhaoManee Birman2 Birman1 Bombay Peterbald Ocicat LaPerm JapaneseBobtail RussianBlue CornishRex Ragdoll2 Ragdoll1 Bengal2 Bengal1 TurkishVan AmericanCurl DevonRex EgyptianMau Sphynx Somali Abyssinian Munchkins Lykoi Chartreux Siberian2 Siberian1 Manx AmericanWirehair NorwegianForestCat MaineCoon ScottishFold2 ScottishFold1 SelkirkRex BritishShorthair Persian2 Persian1 Chr. B3 (Mb) Fst-based Haplotype-based ROH (1, 2, 5, 10, 20Mb) Eastern Breeds without Birman Size: 2.9 Mb 5 genes NDN, SNRPN, UBE3A, ATP10A, GABRB3 -0.04 -0.02 0.00 0.02 0.04 0.06 0.08 -0.15-0.10-0.050.000.05 PC1 PC2 Birman a. -0.15-0.10-0.050.000.05 PC3 b. -0.04 -0.02 0.00 0.02 0.04 0.06 0.08 -0.15-0.10-0.050.000.05 PC2 PC3 Bengal d. -0.06-0.04-0.020.000.020.04 PC4 e.
  29. 29. 0 143 Siamese Korat Burmese2 Burmese1 Oriental KhaoManee Birman2 Birman1 Bombay Peterbald Ocicat LaPerm JapaneseBobtail RussianBlue CornishRex Ragdoll2 Ragdoll1 Bengal2 Bengal1 TurkishVan AmericanCurl DevonRex EgyptianMau Sphynx Somali Abyssinian Munchkins Lykoi Chartreux Siberian2 Siberian1 Manx AmericanWirehair NorwegianForestCat MaineCoon ScottishFold2 ScottishFold1 SelkirkRex BritishShorthair Persian2 Persian1 Chr. B4 (Mb) Fst-based Haplotype-based ROH KRT71 ALX1 (1, 2, 5, 10, 20Mb) 0 143 Siamese Korat Burmese2 Burmese1 Oriental KhaoManee Birman2 Birman1 Bombay Peterbald Ocicat LaPerm JapaneseBobtail RussianBlue CornishRex Ragdoll2 Ragdoll1 Bengal2 Bengal1 TurkishVan AmericanCurl DevonRex EgyptianMau Sphynx Somali Abyssinian Munchkins Lykoi Chartreux Siberian2 Siberian1 Manx AmericanWirehair NorwegianForestCat MaineCoon ScottishFold2 ScottishFold1 SelkirkRex BritishShorthair Persian2 Persian1 Chr. B4 (Mb) Fst-based Haplotype-based ROH KRT71 ALX1 (1, 2, 5, 10, 20Mb) Bengal Breed Size: 6.3 Mb 80 genes OR10P1, ITGA7, BLOC1S1, RDH5, CD63, GDF11, ORMDL2, MMP19, PYM1, DGKA, PMEL, CDK2, RAB5B, SUOX, IKZF4, RPS26, ERBB3, ZC3H10, ESYT1, MYL6B, SMARCC2, RNF41, NABP2, SLC39A5 …etc
  30. 30. General view of selection
  31. 31. 0 241Chromosome Length (Mb) A1 A2 A3 B1 B2 B3 B4 C1 C2 D1 D2 D3 D4 E1 E2 E3 F1 F2 Fst-based 0 241Chromosome Length (Mb) A1 A2 A3 B1 B2 B3 B4 C1 C2 D1 D2 D3 D4 E1 E2 E3 F1 F2 Haplotype-based 0 241Chromosome Length (Mb) A1 A2 A3 B1 B2 B3 B4 C1 C2 D1 D2 D3 D4 E1 E2 E3 F1 F2 Fst-based Haplotype-based 273 candidate regions 317 candidate regions 590 candidate regions Genomic landscape of selection
  32. 32. 41/789 273 10/275 155 33/744 695 5/169 583 Breeds/Samples Fst-based Sweeps 0 241Chromosome Length (Mb) A1 A2 A3 B1 B2 B3 B4 C1 C2 D1 D2 D3 D4 E1 E2 E3 F1 F2 Fst-based 0 241Chromosome Length (Mb) A1 A2 A3 B1 B2 B3 B4 C1 C2 D1 D2 D3 D4 E1 E2 E3 F1 F2 Haplotype-based 0 A1 A2 A3 B1 B2 B3 B4 C1 C2 D1 D2 D3 D4 E1 E2 E3 F1 F2 41/789 273 10/275 155 Breeds/Samples Fst-based Sweeps
  33. 33. What is next?
  34. 34. Leslie A. Lyons, PhD Department of Veterinary Medicine and Surgery Acknowledgment Mona Abdi, M.Sc. Department of Biological Sciences
  35. 35. Disclaimer Figures, photos, and graphs in my presentations 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 presentations a violation of their copy rights, please contact me via email. hhalhaddad@gmail.com

×