Abstract
BackgroundValgus-varus deformity (VVD) is a lateral or middle deviation of the tibiotarsus or tarsometatarsus, which is associated with compromised growth, worse bone quality and abnormal changes in serum indicators in broilers. To investigate the genetic basis of VVD, a genome wide association study (GWAS) was performed to identify candidate genes and pathways that are responsible for VVD leg disease, serum indicators and growth performance in broilers.ResultsIn total, VVD phenotype, seven serum indicators and three growth traits were measured for 126 VVD broilers (case group) and 122 sound broilers (control group) based on a high throughput genome wide genotyping-by-sequencing (GBS) method. After quality control 233 samples (113 sound broilers and 120 VVD birds) and 256,599 single nucleotide polymorphisms (SNPs) markers were used for further analysis. As a result, a total of 5 SNPs were detected suggestively significantly associated with VVD and 70 candidate genes were identified that included or adjacent to these significant SNPs. In addition, 43 SNPs located on Chr24 (0.22 Mb - 1.79 Mb) were genome-wide significantly associated with serum alkaline phosphatase (ALP) and 38 candidate genes were identified. Functional enrichment analysis showed that these genes are involved in two Gene Ontology (GO) terms related to bone development (cartilage development and cartilage condensation) and two pathways related to skeletal development (Toll−like receptor signaling pathway and p53 signaling pathway). BARX2 (BARX homeobox 2) and Panx3 (Pannexin 3) related to skeleton diseases and bone quality were obtained according to functional analysis. According to the integration of GWAS with transcriptome analysis, HYLS1 (HYLS1 centriolar and ciliogenesis associated) was an important susceptibility gene.ConclusionsThe results provide some reference for understanding the relationship between metabolic mechanism of ALP and pathogenesis of VVD, which will provide a theoretical basis for disease-resistant breeding of chicken leg soundness.
Highlights
Valgus-varus deformity (VVD) is a lateral or middle deviation of the tibiotarsus or tarsometatarsus, which is associated with compromised growth, worse bone quality and abnormal changes in serum indicators in broilers
All Single nucleotide polymorphism (SNP) were uniformly distributed on each chromosome and these SNPs are mostly located in intron (Fig. S1) and intergenic regions (Fig. S2)
For VVD, the manhattan and QQ plots indicated that there was no significant SNP associated with VVD clinical phenotype (Fig. 1)
Summary
Valgus-varus deformity (VVD) is a lateral or middle deviation of the tibiotarsus or tarsometatarsus, which is associated with compromised growth, worse bone quality and abnormal changes in serum indicators in broilers. Guo et al BMC Genomics (2022) 23:26 tibiotarsal bone that results in deviation of the tarsometatarsus [1] It has caused severe economic losses for the broiler industry and physical distress in broilers [2, 3]. Previous study showed that VVD had compromised growth, worse bone quality, calcification disorders and abnormal changes in serum lipid indicators, serum calcium (Ca), phosphorus (P) and serum alkaline phosphatase (ALP) levels [4]. Shank length and girth are two important traits for the development of skeleton in broiler [8, 9] These traits are directly or indirectly associated with VVD in broiler
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