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Leizhou goats can be classified into tall and short types based on their size and habits. The tall Leizhou goats are well-suited for grazing management due to their robust physique, while the dwarf types are smaller, grow rapidly, and are more appropriate for feeding management systems. In this study, whole-genome resequencing was conducted to identify genomic variants in 15 Tall-legged (TL) and 15 Short-legged (SL) Leizhou goats, yielding 8,641,229 high-quality SNPs in the Leizhou goat genome. Phylogenetic tree and principal component analyses revealed obvious genetic differentiation between the two groups. Fst and θπ analyses identified 420 genes in the TL group and 804 genes in the SL group. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses indicated that the phosphatidylinositol signaling system is associated with growth and development. Additionally, Genome-Wide Association Study (GWAS) analysis identified eight genes linked to leg length, including B4GALT7 and NR1D1. Notably, the NC_030818.1 (g.53666634T > C) variant was significantly associated with leg length traits, where the CC genotype was linked to shorter legs and the TT genotype to longer legs. This study identifies candidate genes and molecular markers, serving as a reference point for breeding and genetic improvement efforts in Leizhou goats and other goat breeds. [ABSTRACT FROM AUTHOR]