Unit of Animal Genomics
ULg
Fonds européen de développement régional
ECBHM resident Workshop – Nantes, 2013
Management of
Inherited Disorders in
Belgian Blue Cattle Breed
Arnaud Sartelet
Unit of Animal Genomics & GIGA-‐R – University of Liège – Belgium Bovine Clinic – University of Liège – Belgium
Unit of Animal Genomics
ULg
Inherited defects in cattle
q Intensive selection
q Extensive use of AI
Ø OUTBURSTS OF INHERITED DEFECTS
q BLAD (90’) = $5 million in US
q Genomic tools improvement
q High throughput genotypingq Next-generation sequencing (NGS)
Unit of Animal Genomics
ULg
Belgian blue cattle breed
q 50 % belgian cattle & 95 % beef cattle
Ø 1.300.000
q 17.000 BBCB herds / 25.000 herds
q Carcass yield = 70 % with 80 % meat
q 99 % calvings by C-section
q Intensive selection for meat production
q Extensive use of AI (50 %)
Unit of Animal Genomics
ULg
Heredo-surveillance in BBCB
COLLABORATION 500 Breeders 200 Vet prac77onners 4 semen providers AWE, Arsia & DGZ 1,200 CASES 1,400 RELATED -‐ Clinic -‐ Necropsy -‐ Imaging -‐ Biochemestry F M V DATA -‐ Epidemiology -‐ Pedigree -‐ Genotyping -‐ Sequencing -‐ Biobank U A G DIAGNOSTIC TESTS: > 22.000 INDIVIDUALS MAPPING (7) MUTATIONS (7) INFORMATIONS: -‐ Scien7fic -‐ Vulgarisa7ons -‐ Con7nuing educa7on -‐ CongressUnit of Animal Genomics
ULg
q Phenotyping
& epidemiological analysis
q Genotyping: SNP technologies
q Genome Wide Association Study
Unit of Animal Genomics
ULg
Genome-wide Haplotype-based
Association Study
BTA 25 – 1,256 SNPs 38 c as es 38 Cases : 50K SNP chip275 AI sires : Bovine HD SNP chip
Unit of Animal Genomics
ULg
q Sequencing
Ø Candidate gene = Sanger sequencing
Ø NGS : whole genome sequencing or capture Ø NGS: transcriptome
q Causative mutation validation
Ø Expression analysis Ø Functional tests
q Diagnostic tests
Ø 5’ exonuclease assay Ø Haplotype-based
Unit of Animal Genomics
ULg
Sanger sequencing
for candidate gene
3.3 Mb RNF11 50 Kb 14 cases Mutant Wild-‐type EXON 2 3’
5’-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ INTRON 1 -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ AG G A A C A A G
CC2 D1 B ZFYVE9 BTF 3L 4 KT I1 2/ TXN D C1 2 RA B3 B N RD 1/ MIR7 61 OSBP L9 EP S1 5 TTC3 9A RN F1 1 C1 or f1 85 CDK N 2C FA F1 D RT A2 ELA VL4 AGBL 4
G A A C A A G EXON 2 3’ 5’-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ INTRON 1 -‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐ G G
Unit of Animal Genomics
ULg
Unit of Animal Genomics
ULg
Inherited defects in BBCB
q Congenital Muscular Dystonia 1 & 2
q Crooked tail syndrom
q Dwarfism
q Hamartoma and osteopetrosis
q Lethal arthrogryposis syndrom
q Prolonged gestation
Unit of Animal Genomics
ULg
Congenital muscular dystonia 1 & 2
q ATP2A1 or SERCA
Ø Sarcoplasmic Ca pump q Death in few weeks
Ø Bronchopneumonia
q SLC6A5
Ø Na/Cl dependent glycine transporter q Death within few hours
Unit of Animal Genomics
ULg
Unit of Animal Genomics
ULg
q MRC2: Extracellular matrix remodelling
q 25 % carriers
q Selective sweep
q 2
ndloss-of-function
Crooked Tail Syndrom
General appearance 0 0,05 0,1 0,15 0,2 0,25 0,3 0,35 0,4 0,45 0,5 0-50 50-55 55-60 60-65 65-70 70-75 75-80 80-85 85-90 D/+ +/+
Unit of Animal Genomics
ULg
Dwarfism
0 10 20 30 40 50 60 0 1 2 3 4 5 6 7 Num be r of c alve s Age (months) 60 70 80 90 100 110 120 100 150 200 250 300 He ight (c m ) Age (days) q RNF11 : A20 complex Ø Growth Ø Inflammation control q 40 % stunted growth q 25 % carriers q Selective sweepUnit of Animal Genomics
ULg
MUT WT
Hamartomas & osteopetrosis
q CLCN7 : Bone resorption /osteoclasts Ø Ostropetrosis
Ø Lysosomal storage disease q NGS : 3 private mutations
q « Fast mutant » q 10 % carriers
Unit of Animal Genomics
ULg
Lethal arthrogryposis syndrom
q PIG-H : GPI-anchor q NGS : transcritpomic q 5 % carriers
Unit of Animal Genomics
ULg
Prolonged gestation
q Gestation length : 14-15 m q Adenohypophyseal hypoplasiaq Mapping IBD – BTA 18 q Haplotype based test q In progress....
Unit of Animal Genomics
ULg
Management of mutant cases
0 50 100 150 200 250 < 2006 2006 2007 2008 2009 2010 2011 2012 Years AP PG HAM DW CTS CMD 2 CMD 1 CMD1 CMD2 CTS DW HAM, PG, AP CTS#2 Number of re corde d c ase s
Unit of Animal Genomics
ULg
Walloonian mortality rate
0 2 4 6 8 10 12 2002 2003 2004 2005 2006 2007 2008 2009 2010 Mortality rate Years 1 2 3 4 5 % 6 BTV-8
Unit of Animal Genomics
ULg
Management of carriers
(AI sires)
0 10 20 30 40 50 60 70 80 90 100 < 2000 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 %Year of birth
≥ 5 4 3 2 1 0
Unit of Animal Genomics
ULg
Management of carriers
(BBCB population)
0 5 10 15 20 25 30 2006 2007 2008 2009 2010 2011 2012 (% ) Years CMD 1(n = 20,979) 0 5 10 15 20 25 30 2007 2008 2009 2010 2011 2012 (% ) Years CMD 2 (n = 21,113) 0 5 10 15 20 25 30 2006 2007 2008 2009 2010 2011 2012 (% ) Years CTS (n = 19,401) 0 5 10 15 20 25 30 2006 2007 2008 2009 2010 2011 2012 (% ) Years DwarOism (n = 16,468) 0 5 10 15 20 25 30 2006 2007 2008 2009 2010 2011 2012 (% ) Years Hamartoma (n = 11,758) 0 5 10 15 20 25 30 2006 2007 2008 2009 2010 2011 2012 (% ) Years Prolonged gestation (n = 6,378)Unit of Animal Genomics
ULg
Heredo-surveillance in cattle...
q Heredo-surveillance platform
Ø Useful tool for highly selected breeds Ø Efficiency of the collaboration
Ø Useful for emerging diseases (BTV, SBV, ...)
q NGS accelerates causative mutation
identification process
q Selection based on males
Ø Complete & rapid disease eradication Ø Slight carrier frequency decrease
Ø Problematic in case of:
§ High carrier frequencies
Unit of Animal Genomics
