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

Genome-Wide Characterization of Genetic Diversity and Population Structure in a Kazakhstani Two-Row Spring Barley Breeding Panel

Barley (Hordeum vulgare L.) is a major cereal in Kazakhstan, where diverse breeding material supports crop improvement. We characterized 86 two-row spring barley accessions from six breeding organizations using the Illumina Infinium 50K Barley SNP Array. Analysis of 29,920 high-quality SNPs revealed moderate diversity (He = 0.346, PIC = 0.278, Shannon = 0.752), with 80.84% of molecular variation occurring within and 19.16% among breeding organizations. A minor allele frequency-free (MAF-free) analysis showed that 95.61% of marker–allele combinations at polymorphic loci were shared by at least two organizations. Although PCA, kinship, and neighbor-joining analyses indicated extensive overlap, discriminant analysis of principal components (DAPC) cluster membership was significantly associated with breeding origin (χ2 = 106.38, Monte Carlo p = 1 × 10–5; bias-corrected Cramér’s V = 0.513), demonstrating substantial but incomplete differentiation among breeding programs. Phenotypic differentiation was evaluated using environment-adjusted genotype BLUPs. All seven traits differed significantly among five DAPC clusters. In a reduced six-trait linear discriminant analysis (LDA) excluding vegetation period, LD1 was associated most strongly with number of kernels per spike, followed by heading time, spike length, and heading-to-maturity time. Leave-one-out cross-validation (LOOCV) accuracy was 36.47%, exceeding the permutation mean of 19.83% but indicating considerable phenotypic overlap. The examined materials therefore constitute a diverse, interconnected breeding panel that may support germplasm management and parent selection and provide a genomic and phenotypic framework for future GWAS, genomic selection, and targeted validation of molecular markers within the represented collections.

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.

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

First breed-pool whole genome sequencing of egyptian sheep: a comprehensive genomic atlas revealing diversity and candidate genes for production and adaptation

This research provides the first extensive breed‑pool whole‑genome sequencing (WGS) analysis across five Egyptian sheep populations: Barki (BAR), Rahmani (RAH), their crossbred offspring (CRS), Ossimi (OSI) and Awassi (AWI). To establish a genomic atlas of the genetic architecture of production and adaptation in Egyptian sheep, providing a baseline for future candidate gene discovery and conservation strategies. Through Illumina sequencing of 120 samples, we compiled a dataset exceeding 470 Gb, with mean coverage depths spanning 24.2x to 41.3x. Variant profiling, functional annotation, KEGG pathway analysis, and independent structural variant analysis were conducted. Phenotypic data were collected and validated through qRT-PCR gene expression analysis. Variant profiling revealed between 11.9 and 17.4 million SNPs per breed after stringent filtering. Heterozygosity patterns (population‑level estimates) differed substantially between groups, recorded at 60.41% in the CRS crossbred versus 74.92–85.01% in the purebred lines. Functional annotation identified conserved enrichment related to xenobiotic detoxification and lipid metabolism. KEGG pathway analysis prioritized the PPAR signalling pathway (map03320) and fatty acid metabolism (map01212) as highly significant (p < 0.0001). Independent structural variant analysis identified distinct genomic hotspots on chromosomes 2, 6 and 18, overlapping candidate genes; FABP4, KAP cluster and MSTN implicated in the regulation of fat deposition and muscle development. Phenotypic data confirmed a high degree of breed divergence (p < 0.001). RAH and CRS individuals reached higher body condition scores (BCS 4.31‑ 4.53) and increased fat deposition, whereas BAR was significantly leaner (BCS 2.53). The highest trimmed meat yields were observed in CRS (23.95 kg) and RAH (18.40 kg) (p < 0.001), with RAH also displaying the highest intramuscular fat content at 4.20%. qRT‑PCR validation showed elevated expression of lipogenic genes (ACACA, FASN and FABP4) in fat‑tailed breeds and differential expression of myogenic regulators (MSTN and IGF‑1) correlating with muscularity variations. The current findings establish a genomic atlas for the genetic architecture of production and adaptation in Egyptian sheep, providing a baseline for future genetic and conservation strategies. Formal selection signature analyses, such as XP‑EHH and iHS are recommended for subsequent studies.

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.

Unravelling the genetic structure and genetic relationships of indigenous Greek sheep breeds using SNP markers

Indigenous sheep of Greece represent important genetic resources shaped by long-term adaptation to diverse environments. However, many populations face demographic decline, genetic erosion, and their genomic diversity remains inadequately characterized. This study presents a comprehensive genome-wide analysis of both recognized and previously uncharacterized indigenous Greek sheep. Newly genotyped data from 36 Greek breeds/populations, one Cypriot breed and one outgroup (Cypriot Mouflon) were combined with previously published genotypes from 85 international breeds and four additional outgroups, analyzing 127 ovine populations in total. To mitigate commercial BeadChip ascertainment bias when evaluating these uncharacterized populations, we utilized genome-wide SNP blocks to assess genetic diversity, reconstruct population structure, estimate effective population sizes, and place them within a broad comparative framework encompassing European, Southwest Asian, and North African breeds. Genome-wide analyses evaluating 46,733 SNPs and 4347 multi-allelic haplotype blocks revealed a distinct ascertainment bias affecting Western and Eastern breeds differently. Mitigating this bias via the block-based approach demonstrated that Greek sheep breeds/populations retain high genetic diversity, despite pronounced heterogeneity. Breeds such as Lesvos, Vlahiko, and Karagouniko exhibited high heterozygosity, low inbreeding, and relatively large effective population sizes, whereas Thraki, Agrinio, Katafygio, Serres, and Argos showed low diversity, elevated inbreeding, and small recent effective population sizes. Greek breeds/populations occupied an intermediate position between Western European and Southwest Asian groups, reflecting their geographic location and historical role in early dispersal routes. Island populations (Cretan breeds, Kasos and Karpathos) formed a cohesive genetic cluster shaped by long-term isolation, while semi-fat-tailed Greek breeds showed close affinities with Middle Eastern and North African populations. Introgression from East Friesian sheep strongly influenced the genomic profile of the Arta breed. This study provides a comprehensive genomic baseline for indigenous Greek and Cypriot sheep, highlighting their high genetic diversity and complex demographic histories. While several breeds represent valuable reservoirs of adaptive variation, others face immediate risk of genetic erosion. These findings provide essential guidance for prioritizing conservation actions and integrating genomic information into sustainable management and breeding strategies.