Genome-wide association study identifies SNPs for growth performance and serum indicators in Valgus-varus deformity broilers (Gallus gallus) using ddGBS sequencing

Abstract

Background 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. 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. Results In 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. Conclusions The 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.

Genome-wide association study of 17 serum biochemical indicators in a chicken F2 resource population

“…The QTL was also identified in the casecontrol-based GWAS study of the AKP trait mentioned in the background with VVD broilers and sound broilers, the candidate genes located in the QTL were involved in the skeletal development and bone disease. Genetic variation loci of ST3GAL4 gene located in the QTL were closely related to AKP in VVD broilers in their subsequent study which indicated ST3GAL4 plays an important role in serum AKP and the skeletal development [3].…”

“…Valgus-varus deformity (VVD) is a leg disease which lateral or middle deviation of the tibiotarsus or tarsometatarsus, accompanied by abnormal changes in serum AKP levels. Case-control (VVD broilers-sound broilers)based GWAS identified 43 SNPs located on Chr24 (0.22 Mb − 1.79 Mb) that were significantly associated with AKP [3]. In the chicken F2 resource population, the direct relationships between AKP levels and candidate genes and corresponding QTLs have not been reported at present.…”

Genetic characteristics and selection signatures between Southern Chinese local and commercial chickens

“…SAMSN1 ( SAM domain, SH3 domain and nuclear localization signals 1 ) is involved in immune responses as well as reproductive and growth processes ( Zhao et al, 2018 ), potentially reflecting the impact of commercial selection practices. HYLS1 ( Hydrolethalus syndrome 1 ) plays a crucial role in cilia formation and stability; it has been identified as a susceptible gene for Valgus-varus deformity (VVD) and is linked to leg integrity ( Guo et al, 2022 ). ROBO3 ( Roundabout guidance receptor 3 ) is implicated in follicle development in hens ( Qin et al, 2015 ).…”

Assembly of Genome and Resequencing Provide Insights into Genetic Differentiation between Parents of Hulong Hybrid Grouper (Epinephelus fuscoguttatus ♀ × E. lanceolatus ♂)

“…In rainbow trout, quantitative trait loci (QTLs) associated with bodyweight gain were detected using genome-wide association (GWA) analysis, and some genes involved in bodyweight gain were enriched in the cell cycle [23]. In broilers (Gallus gallus), researchers discovered that genes involved in the p53-signaling pathway are associated with the growth performance [24]. These genetic differences may be associated with the differences in body size between the brown-marbled grouper and giant grouper.…”