Whole-genome sequencing identifies a homozygous deletion encompassing exons 17 to 23 of the integrin beta 4 gene in a Charolais calf with junctional epidermolysis bullosa.
BACKGROUND
Since 2010, four Charolais calves with a congenital mechanobullous skin disorder that were born in the same herd from consanguineous matings were reported to us. Clinical and histopathological examination revealed lesions that are compatible with junctional epidermolysis bullosa (JEB).


RESULTS
Fifty-four extended regions of homozygosity (>1 Mb) were identified after analysing the whole-genome sequencing (WGS) data from the only case available for DNA sampling at the beginning of the study. Filtering of variants located in these regions for (i) homozygous polymorphisms observed in the WGS data from eight healthy Charolais animals and (ii) homozygous or heterozygous polymorphisms found in the genomes of 234 animals from different breeds did not reveal any deleterious candidate SNPs (single nucleotide polymorphisms) or small indels. Subsequent screening for structural variants in candidate genes located in the same regions identified a homozygous deletion that includes exons 17 to 23 of the integrin beta 4 (ITGB4), a gene that was previously associated with the same defect in humans. Genotyping of a second case and of six parents of affected calves (two sires and four dams) revealed a perfect association between this mutation and the assumed genotypes of the individuals. Mining of Illumina BovineSNP50 Beadchip genotyping data from 6870 Charolais cattle detected only 44 heterozygous animals for a 5.6-Mb haplotype around ITGB4 that was shared with the carriers of the mutation. Interestingly, none of the 16 animals genotyped for the deletion carried the mutation, which suggests a rather recent origin for the mutation.


CONCLUSIONS
In conclusion, we successfully identified the causative mutation for a very rare autosomal recessive mutation with only one case by exploiting the most recent DNA sequencing technologies.
INRA, UMR1313 Génétique Animale et Biologie Intégrative, domaine de Vilvert, Jouy-en-Josas, F-78352, France. pauline.michot@jouy.inra.fr.|ALLICE, 149 rue de Bercy, Paris, F-75012, France. pauline.michot@jouy.inra.fr.
Pauline
P
Michot
Université de Lyon, VetAgro Sup, UPSP 2011-03-101 Interactions Cellules Environnement, 1 avenue Bourgelat, Marcy l'Etoile, F-69280, France. oscar.fantini@vetagro-sup.fr.
Oscar
O
Fantini
Cabinet des Vignes de la Fontaine, 41 rue du faubourg de Moulins, Saint-Pierre le Moutier, F-58240, France. braque.regis@akeonet.com.
Régis
R
Braque
ALLICE, 149 rue de Bercy, Paris, F-75012, France. aubonnet@jouy.inra.fr.|UMR 1198 Biologie du Développement et Reproduction, domaine de Vilvert, Institut National de la Recherche Agronomique, Jouy-en-Josas, F-78352, France. aubonnet@jouy.inra.fr.
Aurélie
A
Allais-Bonnet
INRA, UMR1313 Génétique Animale et Biologie Intégrative, domaine de Vilvert, Jouy-en-Josas, F-78352, France. romain.saintilan@jouy.inra.fr.|ALLICE, 149 rue de Bercy, Paris, F-75012, France. romain.saintilan@jouy.inra.fr.
Romain
R
Saintilan
INRA, UMR1313 Génétique Animale et Biologie Intégrative, domaine de Vilvert, Jouy-en-Josas, F-78352, France. cecile.grohs@jouy.inra.fr.
Cécile
C
Grohs
INRA, UMR1388 GenPhySE, GeT-PlaGe, Castanet-Tolosan, F-31320, France. johanna.barbieri@toulouse.inra.fr.
Johanna
J
Barbieri
LABOGENA DNA, domaine de Vilvert, Jouy-en-Josas, F-78352, France. lucie.genestout@jouy.inra.fr.
Lucie
L
Genestout
Institut de l'Elevage, 149 rue de Bercy, Paris 12, F-75595, France. coralie.danchin@idele.fr.
Coralie
C
Danchin-Burge
Unité de Pathologie du Bétail, Ecole Nationale Vétérinaire d'Alfort, 7 avenue du Général de Gaulle, Maisons-Alfort, F-94704, France. jm.gourreau@gmail.com.
Jean-Marie
JM
Gourreau
INRA, UMR1313 Génétique Animale et Biologie Intégrative, domaine de Vilvert, Jouy-en-Josas, F-78352, France. didier.boichard@jouy.inra.fr.
Didier
D
Boichard
Université de Lyon, VetAgro Sup, UPSP 2011-03-101 Interactions Cellules Environnement, 1 avenue Bourgelat, Marcy l'Etoile, F-69280, France. didier.pin@vetagro-sup.fr.
Didier
D
Pin
INRA, UMR1313 Génétique Animale et Biologie Intégrative, domaine de Vilvert, Jouy-en-Josas, F-78352, France. aurelien.capitan@jouy.inra.fr.|ALLICE, 149 rue de Bercy, Paris, F-75012, France. aurelien.capitan@jouy.inra.fr.
Aurélien
A
Capitan
D000818:Animals; D002417:Cattle; D002418:Cattle Diseases / Q000235:genetics* / Q000473:pathology; D016109:Epidermolysis Bullosa, Junctional / Q000235:genetics / Q000473:pathology / Q000662:veterinary*; D005091:Exons; D005260:Female; D016678:Genome; D006720:Homozygote; D039663:Integrin beta4 / Q000235:genetics*; D008297:Male; D017422:Sequence Analysis, DNA; D017384:Sequence Deletion
D039663:Integrin beta4