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.
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.
Tingxiang Chen, Ting Wang, Wenrui Ye et al.· Animal Genetics· 0 citations
Objective
Litter size is a key trait for evaluating reproductive performance of goats, which can directly influence the breeding efficiency and profitability of production cycles. However, a comprehensive understanding of its genetic architecture, including the causative mutations and their functional impacts, remains scarce, thus hindering its application in precision breed-ing.
Methods
A total of 92 female Leizhou goats were genotyped through whole-genome se-quencing (WGS), and their litter size were measured for three consecutive births. Subsequently, based on the genotype and phenotype data, population genetic structure analysis, selection signature analysis, and genome-wide association study (GWAS) were performed.
Results
We identified a total of 20,802,514 SNPs in the 92 Leizhou goats. Analysis of genetic structure revealed that the high-litter-size group exhibited greater genetic diversity than the low-litter-size group, although no significant genetic differentiation was detected between them. We identified 340 putative selective regions and 346 candidate genes across the genome. A total of 37 candidate genes were identified as being closely associated with reproductive traits, including BMP6, MAPK8, RPTOR, etc. In GWAS results, we identified 63 quantitative trait loci (QTLs) for litter size at suggestive significance (P＜1×10-5). After, 207 candidate genes were annotated, and 4 of them were highlighted that have been previously reported to be associated with reproductive processes (e.g., TMEM100, PDGFD, NLRP9, and ARHGAP22). By integrating the results from both approaches, we identified MAPK8 as a potential candidate gene associated with litter size. Furthermore, our findings from motif recognition, transcrip-tion factor prediction, and previous studies lead us to propose that the BMP6-GATA4-MAPK8 signaling pathway may play a key role in regulating litter size in goats.
Conclusion
Our findings identify several candidate genes and putative associated variants for litter size, providing valuable insights into the genetic basis of reproductive traits in goats.
Da Feng, Siyi Hu, Jian Ma et al.· Animal bioscience· 0 citations
Simple Summary The Jining Grey goat is a Chinese indigenous goat breed valued for its gray coat, high prolificacy, and adaptation to local production systems, but its growth performance still requires genetic improvement. This study used growth records and low-depth whole-genome sequencing from 70 performance-graded goats to search for candidate genomic regions associated with growth traits. We also examined 47 seven-day-old goats from the same project to explore whether prioritized markers showed early-life trait trends. To reduce reliance on any single analysis in a small population, we combined phenotype comparisons, population-structure analysis, selective-sweep scans, genome-wide association analysis, superior-genotype screening, positional annotation, and exploratory genomic prediction. The results identified a 99-SNP candidate marker panel and showed limited physical overlap between growth-associated candidate regions and major selective-sweep regions related to breed background. However, the findings should be interpreted as preliminary because the cohort was small, sequencing depth was low, imputation was performed within the cohort, and the seven-day analysis did not provide independent validation. Overall, this study provides a conservative candidate-marker resource for future validation and for balanced improvement of growth traits while conserving key characteristics of Jining Grey goats.
BACKGROUND
Harness racing performance in horses is a complex polygenic trait influenced by genetic background, breeding history, training, and environment. Understanding genomic patterns shaped by long-term artificial selection provides insights into performance-related traits and breed-specific genomic variation.
AIMS/OBJECTIVES
This study aimed to characterize genomic differentiation, population structure, and candidate genomic regions potentially influenced by historical selection in Standardbred horses using comparative whole-genome sequencing involving diverse horse breeds.
METHODS
Whole-genome sequencing data from 86 horses representing 16 breeds were retrieved from public repositories and processed using a standardized bioinformatics pipeline. Population structure was investigated using principal component analysis (PCA), ADMIXTURE, Neighbor-Joining phylogeny, and ChromoPainter-based haplotype sharing. Genomic diversity was evaluated using runs of homozygosity (ROH) and nucleotide diversity (π), whereas genetic differentiation was assessed using fixation index (FST) analyses with functional annotation.
RESULTS
After quality control, 18,384,176 autosomal SNPs were retained. Standardbred horses consistently formed a distinct genomic group, with principal components 1 and 2 explaining 5.00% and 3.66% of genomic variation, respectively. ADMIXTURE supported K = 2 as the best-supported clustering solution (cross-validation error = 0.523). ROH analyses revealed variation in genome-wide homozygosity among breeds, while FST and nucleotide diversity analyses identified differentiated genomic regions containing candidate genes associated with growth, skeletal development, muscle function, signaling, metabolism, and nervous system function, including LCORL, NCAPG, PDE1A, CDH13, and HTR1A.
CONCLUSION
This comparative whole-genome analysis identified candidate genomic regions potentially shaped by historical selection in Standardbred horses and contributes to understanding genomic differentiation associated with breed history and functional specialization.
I. Moazami, M. Mohammadabadi, H. A. Nanaei et al.· Journal of Equine Veterinary...· 0 citations
This narrative review synthesizes major advances in sheep genetic mapping, functional genomics, and GS relevant to economically important traits to provide researchers, breeders, and students with a balanced, evidence-based resource to guide future genomic improvements in sustainable sheep production.
Mostafa Ghaderi-Zefrehei, Effat Nasre Esfahani, Hassan Amini Pozveh et al.· Frontiers in Genetics· 0 citations
Introduction Commercial spring maize germplasm in northern China has been shaped by five decades of intensive breeding and the continual incorporation of elite domestic and introduced germplasm, but its genetic diversity, pedigree structure, and genomic signatures of selection remain incompletely characterized. Methods We re-sequenced 108 representative inbred lines from China’s commercial spring maize germplasm and combined them with 14 previously published key inbred lines. Population structure, genetic diversity, identity-by-descent, selective sweeps, and haplotype-trait associations were analyzed across seven heterotic groups. Results The 122 inbred lines represented nearly five decades of elite maize germplasm in northern China. Modern breeding materials showed reduced nucleotide diversity, with π decreasing from 1.58 × 10−3 to 1.34 × 10−3, and an increased deleterious mutation burden. We identified 275 Mb of high-impact IBD regions shared among elite germplasm, containing genes associated with flowering, plant architecture, photosynthesis, and grain quality. Selective sweep analyses detected genomic regions associated with agronomic traits including grain quality and floral organ development. Haplotype analyses further revealed natural alleles related to tassel structure, with differential allele frequencies between the SS and TSPT heterotic groups. Discussion These findings provide a genomic resource for northern Chinese commercial maize germplasm and support future heterotic group optimization, marker-assisted breeding, and genomic selection.
Yuhan Song, Hongsen Nong, Zhenyang Liao et al.· Frontiers in Plant Science· 0 citations