Integrated GWAS, TWAS, and functional enrichment reveal candidate genes for claw and hoof traits in Jiangsu Jersey cattle

Abstract

Claw and hoof health directly affects the athletic ability, service life, and production performance of dairy cows. Identifying relevant candidate genes may help elucidate the underlying biological mechanisms and provide targets for subsequent validation. Phenotypic and genomic data from 1,593 Jersey cattle in Jiangsu Province, China, were used to investigate five claw and hoof traits, including foot angle (FA), heel depth (HD), bone quality (BQ), side view of rear legs (SORL), and rear leg rear view (RLRV). Genomic information was generated using low-depth whole-genome sequencing (WGS; 1×, Illumina NovaSeq 6000) and single-nucleotide polymorphism (SNP) genotyping using the GGP Bovine 100 K chip. After alignment, haplotype phasing, and multi-stage genotype imputation, a high-density genome-wide dataset comprising approximately 7.1 million autosomal SNPs was constructed. Based on this dataset, phenotypic characterization, genetic parameter estimation, association analysis, and functional annotation were performed to investigate the genetic basis of claw and hoof conformation traits. All traits had low heritability, with estimates ranging from 0.039 ± 0.028 (FA) to 0.242 ± 0.045 (BQ). A genome-wide association study (GWAS) using a standard mixed linear model identified 23 and 478 significant SNPs for HD and RLRV, respectively, whereas no significant SNPs were detected for FA, BQ, or SORL. A transcriptome-wide association study (TWAS) identified 13 significant named gene–tissue pairs across FA, HD, BQ, and RLRV. Cross-tissue correlations of TWAS Z-scores indicated varying concordance of association patterns across tissues. Downstream functional enrichment analysis showed that the candidate set represented biological processes related to lipid metabolism, neural signaling, and cell adhesion. In this Jiangsu Jersey population, all five claw and hoof traits showed low heritability. GWAS identified 23 and 478 genome-wide significant SNPs for HD and RLRV, respectively, whereas TWAS identified 13 significant named gene–tissue pairs across FA, HD, BQ, and RLRV. Joint interpretation of the association results and downstream functional annotation prioritized ACER1 , MICALL2 , CLDN18 , COL28A1 , SRXN1 , and TIGAR as candidate genes related to epithelial integrity, skeletal and extracellular-matrix organization, and cellular stress responses. Independent population replication and functional validation are required before causal inference or breeding application.