Genome-wide association study of body size traits in dairy goats integrating structural variants.

Body size traits serve as crucial phenotypic indicators of body conformation and growth, showing a close correlation with production performance. To elucidate the genetic basis of these traits and identify potential molecular markers in Saanen dairy goats, we analyzed low-coverage whole-genome sequencing (lcWGS) data from 635 individuals. Following genotype imputation based on an in-house goat reference panel, we obtained 14 million single-nucleotide polymorphisms (SNPs) and 45 thousand structural variants (SVs). Genetic parameters were estimated using SNP data. Subsequently, single-trait (ST) and multi-trait genome-wide association studies (MT-GWAS) were conducted using both SNP and SV datasets. Results indicated that body height, body length, and rump height possess moderate heritability, with positive genetic and phenotypic correlations observed among these traits. ST-GWAS identified 56 significant SNPs and 3 significant SVs, mapping to 30 candidate genes, including TNFSF11, HDAC4, and MURC. Furthermore, MT-GWAS detected 2 significant SNPs and 2 significant SVs missed by ST-GWAS, identifying 4 additional candidate genes (S100A11, LOC108635595, GALNTL6, and FSIP2). Notably, overlapping association signals for body length and rump height were observed near NRXN3 on chromosome 10, with colocalization analysis supporting the existence of a shared causal variant in this region. KEGG enrichment analysis indicated that candidate genes were primarily enriched in fatty acid biosynthesis and related metabolic pathways. In conclusion, this study shows that integrating structural variants into MT-GWAS can reveal association signals beyond those captured by SNPs, providing a theoretical basis for marker-assisted selection and precision breeding for body conformation.