PSIII-13 Uncovering the genetic basis of cleft palate in Boer goats

Abstract Cleft palate is a genetic deformity that can occur in several species, it is the result of the palate of the mouth not fully forming during gestation. This leaves an opening in the mouth that could extend to the nasal cavity, potentially causing the animal to be unable to eat or drink properly. This typically leads to the breeder euthanizing the animal shortly after birth. The objective of this study was to determine the genetic cause of cleft palate in Boer goats and to develop a diagnostic tool that allows producers to select against it. Blood samples (n = 15) were collected from three Boer goat herds. The samples represented six trios and one quad that included sire, dam, and affected kid(s). All affected kids were sired by the same male. Genomic DNA was extracted and used to generate libraries for whole genome sequencing. An average of 179.7 million reads were generated across all samples (range from 151.2 million to 224.4 million reads) resulting in approximately 10X genome coverage per sample. After sequencing, quality filtering was performed using a nextflow pipeline modeled after the germline short variant discovery best practices workflow from the Genome Analysis Toolkit (GATK) software. After filtering, reads were mapped to the Saanen_v1 reference genome. The pipeline called 18,867,792 variants across the 15 samples. Variants were processed using Ensembl Variant Effect Predictor (VEP) to identify potentially high-impact mutations that may be causal. Additional analyses will be used to refine this list of candidate variants for this condition.