Identification and Functional Annotation of Genes Related to Bone Stability in Laying Hens Using Random Forests

• Published in: Genes Vol. 12; no. 5; p. 702
• Main Authors: Jansen, Simon, Baulain, Ulrich, Habig, Christin, Ramzan, Faisal, Schauer, Jens, Schmitt, Armin Otto, Scholz, Armin Manfred, Sharifi, Ahmad Reza, Weigend, Annett, Weigend, Steffen
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 08-05-2021; MDPI
• Subjects: Algorithms; Animals; Avian Proteins - genetics; Bone Density - genetics; Bone diseases; Bone mineral density; Bone strength; Bones; Chickens - physiology; Classification; Decision Trees; Female; Fractures; Gene loci; Genome-Wide Association Study - methods; Genomes; Humerus; Machine learning; Metabolic pathways; Osteoporosis; Phylogenetics; Polymorphism, Single Nucleotide; Population; Quality control; Single-nucleotide polymorphism; Tibiotarsus; United States > US; bone mineral density; single nucleotide polymorphism; skeletal integrity; Random Forests; gene set enrichment analysis; osteoporosis; bone breaking strength
• ISSN: 2073-4425; 2073-4425
• DOI: 10.3390/genes12050702

Skeletal disorders, including fractures and osteoporosis, in laying hens cause major welfare and economic problems. Although genetics have been shown to play a key role in bone integrity, little is yet known about the underlying genetic architecture of the traits. This study aimed to identify genes associated with bone breaking strength and bone mineral density of the tibiotarsus and the humerus in laying hens. Potentially informative single nucleotide polymorphisms (SNP) were identified using Random Forests classification. We then searched for genes known to be related to bone stability in close proximity to the SNPs and identified 16 potential candidates. Some of them had human orthologues. Based on our findings, we can support the assumption that multiple genes determine bone strength, with each of them having a rather small effect, as illustrated by our SNP effect estimates. Furthermore, the enrichment analysis showed that some of these candidates are involved in metabolic pathways critical for bone integrity. In conclusion, the identified candidates represent genes that may play a role in the bone integrity of chickens. Although further studies are needed to determine causality, the genes reported here are promising in terms of alleviating bone disorders in laying hens.