Analysis of DNA Methylation Profiles in Mandibular Condyle of Chicks With Crossed Beaks Using Whole-Genome Bisulfite Sequencing

Abstract

Crossed beaks have been observed in at least 12 chicken strains around the world, which severely impairs their growth and welfare. To explore the intrinsic factor causing crossed beaks, this study measured the length of bilateral mandibular ramus of affected birds, and investigated the genome-wide DNA methylation profiles of normal and affected sides of mandibular condyle. Results showed that the trait was caused by impaired development of unilateral mandibular ramus, which is extended through calcification of mandibular condyle. The methylation levels in the CG contexts were higher than that of CHG and CHH, with the highest methylation level of gene body region, followed by transcription termination sites and downstream. Subsequently, we identified 1,568 differentially methylated regions and 1,317 differentially methylated genes in CG contexts. Functional annotation analysis of Gene Ontology and Kyoto Encyclopedia of Genes and Genomes showed that these genes were involved in bone mineralization and bone morphogenesis. Furthermore, by combining the WGBS and previous RNA-Seq data, 11 overlapped genes were regulated by both long non-coding RNA and DNA methylation. Among them, FIGNL1 is an important gene in calcification of mandibular condyle. Generally, because the affected genes play key roles in maintaining mandibular calcification, these changes may be pivotal factors of crossed beaks.

Genetic Factors That Affect Asymmetric Mandibular Growth—A Systematic Review

“…After the first selection, there were five human studies that met the above-mentioned requirements: two cross-sectional studies [13,18] and three case-control studies [11,19,20]. Four animal studies were also selected: one case-control study [16] and three experimental studies [21][22][23].…”

“…To assess the animal study by Shi et al, (2021) [16], we used the JBI critical appraisal tool: checklist for analytical case-control studies, as this was the only non-experimental study that was conducted in this group. To analyse the remaining animal studies, the SYR-CLE's risk of bias (RoB) tool for animal studies (the Systematic Review Centre for Laboratory Animal Experimentation) was used, which was developed from the Cochrane RoB Tool [17] and adapted to account for differences between aspects of animal and human studies.…”

“…Therefore, it can be assumed that the impact of this gene was confirmed to a moderate degree. [16] investigated the impact of FINGL1 on asymmetry formation. Their publication was a case-control animal study and their study group involved chicks with crossed beaks.…”