A genome-wide association study for diarrhoea sensitivity in newborn rabbits.

Breeding and selection programs in farmed animals that aim to increase disease resistance can provide sustainable approaches to benefit animal welfare, reduce the use of antibiotics, reduce breeding production costs and improve farmers’ profitability. Diarrhoea of newborn rabbits is one of the main causes of pre-weaning death in commercial rabbitries. In this study, we carried out a genome-wide association study to identify genomic regions that encompass variability involved in determining sensitivity to pre-weaning diarrhoea in a commercial rabbit population. The study was based on a case (rabbits affected by diarrhoea) and control (rabbits without any diarrhoea) experimental design within litters produced from 7 bucks and 45 does. A total of 182 affected and 149 healthy newborn rabbits selected from litters that had at least one case and one control were genotyped with the Affymetrix Axiom OrcunSNP Array (199,692 DNA markers). Association analysis was carried out via linear mixed models, as implemented in GEMMA v.0.98. A main peak of associated single nucleotide polymorphisms (SNPs) and other suggestively associated SNPs were identified in a few rabbit chromosomes. Additional cases and controls from another cohort of the same rabbit population were subsequently used to genotype the most significant SNP and validate the obtained results. Whole genome resequencing of three cases and three controls identified a few candidate causative mutations. These results are useful to implement a marker assisted selection program with the aim to improve resistance against pre-weaning diarrhoea in newborn rabbits.