Analysis of Population Structure and Selection Signature in Wadi Sheep Based on Resequencing Data

Genome-Wide Resequencing Reveals Genetic Diversity and Selection Signatures in Two Indigenous Goat Populations From Xizang.

Zhangmu goats and Chentang black goats are valuable local goat genetic resources in Shigatse, Xizang. Due to long-term geographic isolation and small population size, their genetic diversity and adaptive genetic basis remain poorly understood. In this study, whole-genome resequencing was performed on 30 Zhangmu goats and 30 Chentang black goats. By calculating indicators such as observed heterozygosity (HO), expected heterozygosity (HE), nucleotide diversity (π), and inbreeding coefficient (FIS), the genetic diversity of the two populations was comprehensively assessed, and their selection signatures were analyzed using both Fst and XP-CLR. The results showed that both Zhangmu goats and Chentang black goats exhibited relatively low but detectable levels of genetic diversity, with clear genetic differentiation from wild goats. Population structure analysis indicated that the two indigenous populations possessed relatively independent genetic backgrounds. Combined Fst and XP-CLR analyses identified multiple candidate genes associated with hypoxia adaptation (ARNT), immune response (CD274, PTPN7), growth and development (FGF5, MYOM3), and reproductive regulation (GDF5, MEIOB). Functional enrichment analysis revealed that these candidate genes were mainly enriched in GO terms such as nucleoplasm, and in pathways such as the calcium signaling pathway and propanoate metabolism. These results provide genomic insights into the genetic characteristics of Zhangmu goats and Chentang black goats, and offer a theoretical basis for the conservation and sustainable utilization of indigenous goat genetic resources in Xizang.

Deciphering genetic diversity and selection footprints in Rathi cattle through ddRAD-based genome-wide analysis

Analysis of genetic structure and genetic diversity in Diannan small-ear pig.

Identifying selection signatures associated with production traits in Matou goats using whole-genome sequencing

Abstract Investigating the genetic attributes of indigenous goat breeds is crucial for their conservation and breeding. The Matou goat, a valued native breed of Southern China, is characterized by high meat quality and reproductive efficiency, representing an important genetic resource for livestock production. Its genetic basis underlying productive traits remains unclear at the whole-genome level. Therefore, this study aimed to elucidate its genomic diversity and selection signatures with whole-genome sequencing (WGS), in order to provide a basis for its future conservation and breeding. Population structure analyses, including principal component analysis, phylogenetic tree construction, and admixture analysis, revealed that the 128 sampled individuals could be divided into two subgroups. One subgroup exhibited greater genetic diversity, as reflected by higher heterozygosity and lower inbreeding coefficients, along with a higher frequency of private alleles indicative of a more closed breeding history. The slower linkage disequilibrium decay observed in this subgroup suggests it has undergone stronger selection. By integrating Fst, XP‑CLR, and XP‑EHH analyses, we identified 215 genes within 306 candidate regions under selection. Several of these genes (ARHGAP31, CHURC1, ITGA11, and GFOD1) harbor variants that overlap with QTLs and are associated with production traits in livestock. These findings provide a basis for conservation and breeding of the Matou goat.

Integrating whole-genome resequencing data reveals adaptive selection signatures under extreme environments of goat populations in China.

With the increasing frequency of extreme weather events globally, livestock are facing ever-increasing demands for environmental adaptability. Some goat populations have demonstrated remarkable adaptability under long-term extreme environmental stress, and their genomes retain characteristic genetic imprints formed by adaptive evolution. This study integrated whole-genome resequencing data from 496 individuals from 29 endemic goat populations in China, along with data from 11 environmental factors. Through signal selection analysis and genome-environment association analysis, we identified 262 candidate genes associated with environmental adaptation. Subsequently, we screened Chinese goat populations in extreme environments based on environmental data. We used the FST and θπ methods to scan the genomes of these goat populations. In four extreme environments (high elevation, hot, and arid), 95, 74, and 162 candidate genes were identified, respectively. Based on research related to environmental adaptation, we found that genes such as FGF5, CAMK4, COL4A3BP, and CACNG4 may play important roles in goat adaptation to extreme environments. This study not only deepens our understanding of the evolutionary mechanisms of environmental adaptation in Chinese goats, but also provides important theoretical basis for goat stress resistance breeding and germplasm resource conservation.

Whole-Genome Resequencing Reveals Selection Signatures Associated With Lambskin Patterns in Hu Sheep.

In China, Hu sheep lambskin quality is largely determined by wool curvature, with wavy-wool lambs producing higher-quality pelts than straight-wool lambs. However, the genetic mechanisms underlying wool curvature formation remain poorly understood. To address this knowledge gap, we conducted whole-genome resequencing and transcriptomic analyses to identify candidate genes associated with wool curvature in Hu sheep. Phenotypic records from 3047 Hu lambs identified significant differences between wavy- and straight-wool groups. Twenty representative animals (10 per group) were selected for whole-genome resequencing. Selective sweep analyses based on the fixation index (FST), absolute log2-transformed nucleotide diversity ratio [|log2(π ratio)|], and Tajima's D (TajD) identified 157 genomic windows under positive selection. Four major genomic regions showing strong selective signatures were located on chromosomes 4, 7, 13, and 18. Several biologically relevant candidate genes were identified within these regions, including KRTDAP, FGF2, FGF7, OCLN, MAPK1, SHC4, LAMA2, and COL9A3. Functional enrichment analysis indicated that these genes are primarily associated with extracellular matrix (ECM) organization, focal adhesion, PI3K-Akt, MAPK, and Ras signaling pathways. In addition, RNA sequencing (RNA-seq) data from an independent cohort of eight lambs were integrated with genomic selection signals. This integrative analysis identified 61 overlapping genes, from which 12 high-confidence candidate genes were prioritized, including LUM, COL6A1, SPARC, ITGA11, and DCLK1. These findings highlight genomic regions and candidate genes potentially associated with ECM remodeling and other biological processes relevant to lambskin pattern formation, providing valuable genomic resources for future functional studies and marker-assisted selection in Hu sheep.