Abstract
SummaryAn embryonic lethal mutation in chicken named cleft primary palate (cpp) is inherited in an autosomal recessive mode and results in a severely truncated upper beak. In this study, genotyping and sequencing techniques were employed to advance our genetic and genomic knowledge of the mutation’s chromosomal location, candidate region and possible causative element using a congenic inbred line. Herein, the candidate region for the cpp developmental mutation was established as a ca. 5.1 Mb region of chicken chromosome 11 (GGA 11) through the use of a 600K Affymetrix SNP array. The SNPs identified from this array linked to cpp were used to genotype individuals from the congenic inbred line over several generations and thereby fine‐map the causative region resulting in an approximately 200 kb size reduction. This candidate region (4.9 Mb) was sequenced via capture array in a cohort of 24 individuals, including carriers, mutants and their wild type (wt) siblings. Interestingly, the GGA 11 region for cpp encompasses the predicted centromere location and is thus unlikely to be highly disrupted by further recombination. Here we report on the variation unique to the cpp mutation, i.e. single‐nucleotide variants and insertions or deletions. Although the candidate region contains several genes of interest with regard to the cpp phenotype, only one cpp‐linked variant was predicted to have a significant physiological effect by causing a frameshift mutation in ESRP2, which has a role in tissue‐specific splicing during development.
Highlights
The intricacies of facial development have long held interest for researchers as a high incidence of spontaneous congenital facial malformations in humans is observed worldwide
The cpp mutation is inherited in an autosomal recessive fashion with complete penetrance and is embryonic lethal between 17 and 20 days of incubation (Abbott & MacCabe 1966)
Samples were derived from the UCD cpp.003 developmental congenic inbred chicken line
Summary
The intricacies of facial development have long held interest for researchers as a high incidence of spontaneous congenital facial malformations in humans is observed worldwide. Craniofacial anomalies, such as clefting of the lip and/or palate, may be caused by chemical or environmental factors during embryonic development and can be due to genetic factors as well (Schutte & Murray 1999; Cobourne 2004; Schock et al 2016). The homozygous sc mutation, as its name implies, results in absence of scales, as well as foot pads, spurs and most feather follicles, but otherwise does not cause craniofacial or limb defects
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