Screening of SNP Loci Related to Leg Length Trait in Leizhou Goats Based on Whole-Genome Resequencing

Abstract

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.

Keywords: Leizhou goat; SNPs; leg length trait; whole-genome resequencing.

Figure 1

Short-legged (SL) Leizhou goats: (a); tall-legged (TL) Leizhou goats: (b).

Figure 2

Population structure analysis of Leizhou goats: (a) phylogenetic tree of 30 Leizhou goats; (b) PCA diagram of principal component analysis of 30 Leizhou goats; (c) structure of 30 Leizhou goats.

Figure 3

Selection elimination analysis of Leizhou goat populations: (a) autosomal Fst distribution of TL vs. SL group in Leizhou goat; (b) Fst ratio of Leizhou goat TL vs. SL group; (c) Leizhou goat TL vs. SL group Fst and θπ selection elimination analysis plot (The gray dashed line represents the threshold line for selection signals).

Figure 4

Functional enrichment analysis of selected genes in SL group was performed using GO and KEGG databases: (a) GO enrichment analysis of selected genes for leg length traits in Leizhou goats in SL group; (b) KEGG enrichment analysis of leg length trait of Leizhou goat in SL group (* indicates p < 0.001, suggesting a very strong significance).

Figure 5

Functional enrichment analysis of selected genes in TL group was performed using GO and KEGG databases: (a) GO enrichment analysis of selected genes for leg length traits of Leizhou goats in TL group; (b) KEGG enrichment analysis of selected genes for leg length traits of Leizhou goats in TL group (* indicates p < 0.001, suggesting a very strong significance).

Figure 6

(a): Genome-wide association analysis of leg length in Leizhou goats: (b): Manhattan and Q-Q plots (Color changes in the plot are where chromosomes change).

Figure 7

(a) Polymor-208 phisms of candidate SNPs for DNA pooling detection (only some of them are listed); (b) 209 NC_030818.1 53666634 T > C) electropherogram after digestion; (c) NC_030818.1 (g. Sequencing re-210 sults of 53666634 T > C) locus.