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Search Results (696)

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12 pages, 483 KB  
Article
Association of SLC11A1 3′UTR (GT)n Microsatellite Polymorphisms with Resistance to Paratuberculosis in Sheep
by Antonia Mataragka, Anastasios Klavdianos Papastathis and John Ikonomopoulos
Pathogens 2025, 14(11), 1150; https://doi.org/10.3390/pathogens14111150 - 12 Nov 2025
Abstract
Paratuberculosis (Johne’s disease) is a chronic enteric infection of ruminants caused by Mycobacterium avium subsp. paratuberculosis (MAP), leading to significant economic losses in livestock production. While the solute carrier family 11 member 1 (SLC11A1) gene has been implicated in resistance to [...] Read more.
Paratuberculosis (Johne’s disease) is a chronic enteric infection of ruminants caused by Mycobacterium avium subsp. paratuberculosis (MAP), leading to significant economic losses in livestock production. While the solute carrier family 11 member 1 (SLC11A1) gene has been implicated in resistance to intracellular pathogens in several species, its role in ovine paratuberculosis remains largely uncharacterized. The present study investigated whether polymorphic variation in the SLC11A1 3′ untranslated region (3′UTR) (GT)n microsatellite is associated with resistance or susceptibility to MAP infection in sheep. A total of 138 sheep from three breeds (Karagouniki, Boutsika, and Chios) were genotyped. Gene expression analysis was subsequently performed on a subset of 53 animals, which comprised rigorously phenotyped MAP-resistant (n = 18) and MAP-sensitive (n = 35) individuals from the Karagouniki breed. Four predominant alleles, (GT)21, (GT)22, (GT)23, and (GT)24, were identified. The (GT)21 and (GT)23 alleles were significantly enriched among resistant sheep, while (GT)22 and (GT)24 were more frequent in sensitive animals (χ2 = 12.4, p = 0.006; Cramér’s V = 0.38). No significant differences in basal SLC11A1 mRNA expression were detected between phenotypic groups. These findings extend previous GWAS results in sheep by providing the first allele-level evidence linking SLC11A1 3′UTR microsatellite polymorphisms to paratuberculosis resistance in sheep. Although limited by sample size and single-breed representation, the results offer a foundation for future functional and genomic selection studies aimed at enhancing disease resilience in small ruminants. Full article
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19 pages, 3783 KB  
Article
FGF22 Secreted by Hair Papilla Cells Regulates Hair Follicle Stem Cell Proliferation and Differentiation
by Yu Luo, Tong Xiao, Binpeng Xi, Yufang Song, Zengkui Lu, Chao Yuan, Jianbin Liu and Tingting Guo
Biomolecules 2025, 15(11), 1560; https://doi.org/10.3390/biom15111560 - 6 Nov 2025
Viewed by 307
Abstract
Hair follicle stem cells (HFSCs) are resident stem cells within hair follicles (HFs) that possess self-renewal and differentiation capacities, serving as a critical model for regenerative medicine research. Their dynamic interaction with dermal papilla cells (DPCs) plays a decisive role in HF development [...] Read more.
Hair follicle stem cells (HFSCs) are resident stem cells within hair follicles (HFs) that possess self-renewal and differentiation capacities, serving as a critical model for regenerative medicine research. Their dynamic interaction with dermal papilla cells (DPCs) plays a decisive role in HF development and cycling. FGF22 is a paracrine fibroblast growth factor that can regulate the proliferation, differentiation and migration of epithelial cells. This study established a DPC-HFSC co-culture system, revealing that FGF22 overexpression in DPCs significantly upregulated FGFR1/FGFR2 mRNA expression levels in HFSCs (p < 0.05), with a 1.67-fold increase in EdU-positive cell proportion (p < 0.01). CCK-8 assays demonstrated markedly enhanced HFSC viability (p < 0.01), with a 17% reduction in HFSC apoptosis (p < 0.05). Conversely, FGF22 knockout downregulated FGFR1/FGFR2 expression (p < 0.05), reduced HFSC proliferation capacity by 25% (p < 0.01), and increased HFSC apoptosis levels by 1.81-fold (p < 0.05). In addition, FGF22 overexpression promotes the proliferation and differentiation of HFSCs by activating Wnt/β-Catenin, Sonic Hedgehog (Shh) and Notch signaling pathways, or inhibiting BMP signaling pathways. Knockout of FGF22 weakens these processes and inhibits the activation and differentiation of HFSCs. This study, through the DPCs-HFSCs co-culture system, revealed the regulatory mechanism of FGF22 secreted by DPCs on the proliferation and differentiation of HFSCs, thereby providing theoretical references for fields such as fine-wool sheep breeding, human regenerative medicine, and hair loss treatment. Full article
(This article belongs to the Section Molecular Biology)
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25 pages, 1044 KB  
Article
Antibiotic Susceptibility of Autochthonous Enterococcus Strain Biotypes Prevailing in Sheep Milk from Native Epirus Breeds Before and After Mild Thermization in View of Their Inclusion in a Complex Natural Cheese Starter Culture
by John Samelis and Athanasia Kakouri
Appl. Microbiol. 2025, 5(4), 125; https://doi.org/10.3390/applmicrobiol5040125 - 6 Nov 2025
Viewed by 145
Abstract
Autochthonous enterococci surviving mild thermization of raw milk (RM) before traditional Greek cheese processing may simultaneously comprise safe and virulent thermoduric strains with multiple antibiotic resistances (ARs). Therefore, this study biotyped and then compared the ARs of 60 Enterococcus isolates from two antilisterial [...] Read more.
Autochthonous enterococci surviving mild thermization of raw milk (RM) before traditional Greek cheese processing may simultaneously comprise safe and virulent thermoduric strains with multiple antibiotic resistances (ARs). Therefore, this study biotyped and then compared the ARs of 60 Enterococcus isolates from two antilisterial sheep milks of native Epirus breeds before (RM) and after (TM) thermization at 65 °C for 30 s; the RM isolates were previously genotyped and evaluated for primary safety traits, namely, hemolytic activity, vanA/vanB, cytolysin, and virulence genes, by molecular methods. Biochemically typical and atypical strains of Enterococcus faecium (six biotypes), E. durans (five biotypes), E. faecalis (two biotypes), and E. hirae (one biotype), which were subdominant to other LAB species in RM (19 isolates), prevailed in TM (41 isolates). E. faecium biotypes 1A, 1D, and 1H included multiple-Ent+ (entA/entB/entP or entA/entB) strains with strong antilisterial CFS activity, whereas E. faecium 1X (entA), E. durans 2A, 2B, 2C, and 2X (entA/entP or entP), E. faecalis 3B, and E. hirae 4A (entA) biotypes displayed direct in vitro antilisterial activity only. Biotypes 1D, 1X, and 2A were selected in TM. All E. faecium/durans isolates were susceptible to vancomycin, but the m-Ent + E. faecium biotype 1A and 1D strains were resistant to penicillin, erythromycin, ciprofloxacin, and ampicillin. In contrast, all biotype 1X isolates were susceptible to all antibiotics tested. All E. faecalis and most E. durans isolates were resistant to penicillin but susceptible to erythromycin and ciprofloxacin. Biotype 2X isolates and one virulent (ace; gelE) E. faecalis isolate from RM were tetracycline-resistant. A sporadic RM isolate of E. hirae that was resistant to penicillin and vancomycin was not retrieved from the counterpart TM, but the inclusion of three vancomycin-resistant isolates from TM in the primary biotype 3B of E. faecalis was a cause for concern. In conclusion, based on the results, antibiotic-susceptible representatives of all strain biotypes of the E. faecium/durans group, as well as antagonistic m-Ent+ E. faecium strains from sheep milk that were susceptible to vancomycin and ampicillin and lacking virulence genes, can be included in safe complex natural starters to be developed for onsite use in traditional Greek hard cheese technologies. Full article
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13 pages, 1157 KB  
Article
Evaluation of Total Eosinophil Counts, Serum Allergen-Specific IgE and Related Cytokines in Dogs with Atopic Dermatitis
by Min-Joo Chae, Min-Hee Kang and Hee-Myung Park
Animals 2025, 15(21), 3219; https://doi.org/10.3390/ani15213219 - 5 Nov 2025
Viewed by 243
Abstract
Canine atopic dermatitis (AD) is a chronic allergic skin disease in which various immunological markers have been investigated. While peripheral eosinophil counts, serum allergen-specific immunoglobulin E (IgE), and cytokines have each been evaluated in allergic disorders, their simultaneous assessment in dogs with AD [...] Read more.
Canine atopic dermatitis (AD) is a chronic allergic skin disease in which various immunological markers have been investigated. While peripheral eosinophil counts, serum allergen-specific immunoglobulin E (IgE), and cytokines have each been evaluated in allergic disorders, their simultaneous assessment in dogs with AD has rarely been reported in Korea. This study aimed to evaluate the diagnostic and clinical utility of these parameters in affected dogs. A total of 93 dogs were included between August 2019 and February 2020, comprising 65 dogs diagnosed with AD and 28 healthy controls. Clinical information, peripheral blood eosinophil counts and ratios, serum allergen-specific IgE using a multiple allergen panel (60 allergens), and cytokines related to T helper 2 (Th2) and T regulatory (Treg) cells (IL-4, IL-13, IL-31, TGF-β1) were analyzed. The mean age of AD dogs was 6.34 ± 3.99 years, with a predominance of small breeds and males. Eosinophil counts and ratios showed no significant difference between groups. In contrast, allergen-specific IgE levels were significantly elevated for several allergens, including Dermatophagoides pteronyssinus, Acarus siro, Tyrophagus putrescentiae, alder/birch, hazel, oak, cladosporium, and selected dietary antigens (pea, soybean, pumpkin, apple) (p < 0.05). Sensitization rates were also higher for Acarus siro, Tyrophagus putrescentiae, oak, and sheep sorrel (p < 0.05). Th2-related cytokines tended to increase and TGF-β1 tended to decrease in AD dogs, though without statistical significance. These findings indicate that peripheral eosinophil counts have limited diagnostic value, whereas allergen-specific IgE testing provides clinically useful information for the diagnosis and management of canine AD. Further research stratifying disease stages and assessing local tissue cytokine expression is warranted. Full article
(This article belongs to the Section Veterinary Clinical Studies)
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16 pages, 1111 KB  
Article
Two-Stage Machine Learning-Based GWAS for Wool Traits in Central Anatolian Merino Sheep
by Yunus Arzık, Mehmet Kizilaslan, Sedat Behrem, Simge Tütenk and Mehmet Ulaş Çınar
Agriculture 2025, 15(21), 2287; https://doi.org/10.3390/agriculture15212287 - 3 Nov 2025
Viewed by 379
Abstract
Wool traits such as fiber diameter, fiber length, and greasy fleece yield are economically significant characteristics in sheep breeding programs. Traditional genome-wide association studies (GWAS) have identified relevant genomic regions but often fail to capture the non-linear and polygenic architecture underlying these traits. [...] Read more.
Wool traits such as fiber diameter, fiber length, and greasy fleece yield are economically significant characteristics in sheep breeding programs. Traditional genome-wide association studies (GWAS) have identified relevant genomic regions but often fail to capture the non-linear and polygenic architecture underlying these traits. In this study, we implemented a two-stage machine learning (ML)-based GWAS framework to dissect the genetic basis of wool traits in Central Anatolian Merino sheep. Phenotypic records were collected from 228 animals, genotyped with the Illumina OvineSNP50 BeadChip. In the first stage, feature selection was conducted using LASSO, Ridge Regression, and Elastic Net, generating a consensus SNP panel per trait. In the second stage, association modeling with Random Forest and Support Vector Regression (SVR) identified the most predictive models (R2 up to 0.86). Candidate gene annotation highlighted biologically relevant loci: MTHFD2L and EPGN (folate metabolism and keratinocyte proliferation) for fiber diameter; COL5A2, COL3A1, ITFG1, and ELMO1 (extracellular matrix integrity and actin remodeling) for staple length; and FAP, DPP4, PLCH1, and NPTX1 (extracellular matrix remodeling, proteolysis, and sebaceous gland function) for greasy fleece yield. These findings demonstrate the utility of ML-enhanced GWAS pipelines in identifying biologically meaningful markers and propose novel targets for genomic selection strategies to improve wool quality and yield in indigenous sheep populations. Full article
(This article belongs to the Special Issue Genetic Diversity, Adaptation and Evolution of Livestock)
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18 pages, 1647 KB  
Article
Thiamine Diphosphate Supplementation as a Heat-Stress Mitigation Strategy for Hair Male and Female Lambs in Feedlot: Physiological Responses, Growth Performance, and Carcass Traits
by Ulises Macías-Cruz, German Castillo Cristóbal, Leonel Avendaño-Reyes, María de los Ángeles López-Baca, José A. Roque-Jiménez, Miguel Mellado, César A. Meza-Herrera, Ricardo Vicente-Pérez, Marisol López-Romero and Nallely Rivero-Pérez
Animals 2025, 15(21), 3143; https://doi.org/10.3390/ani15213143 - 29 Oct 2025
Viewed by 271
Abstract
Twenty Dorper × Katahdin lambs (10 males and 10 females) were distributed in a 2 × 2 factorial arrangement under a randomized complete block design to evaluate the effects of thiamine diphosphate (TD) supplementation (0 vs. 250 mg/kg feed) and gender (males vs. [...] Read more.
Twenty Dorper × Katahdin lambs (10 males and 10 females) were distributed in a 2 × 2 factorial arrangement under a randomized complete block design to evaluate the effects of thiamine diphosphate (TD) supplementation (0 vs. 250 mg/kg feed) and gender (males vs. females) on physiological responses, feedlot performance, carcass characteristics, and meat quality in a hot desert environment. The average temperature and temperature–humidity index recorded during the study were 33.60 °C and 35.89 units, respectively, indicating an extremely severe heat stress environment for lambs. Study variables were not affected (p ≥ 0.12) by the TD × gender interaction, except for dry matter intake (DMI; p = 0.02) and some head temperatures (p ≤ 0.05) and carcass zoometric measurements (p ≤ 0.05). In females, but not in males, TD decreased DMI and increased thorax depth, as well as eye, ear, and forehead temperatures. Overall, TD increased (p ≤ 0.05) surface temperatures of neck, shoulder, loin, rump, forelimb, testicles, vulva, anus, and perineum without affecting (p ≥ 0.58) rectal temperature and respiratory rate. Supplemental TD did not affect (p ≥ 0.16) growth rate, feed efficiency, carcass weight and yield, Longissimus thoracic muscle area, backfat thickness, internal fat deposition, wholesale cut yields, and meat quality traits. In conclusion, in hair ewe lambs but not in male lambs, TD supplementation at a dose of 250 mg/kg of feed in the fattening diet is an HS mitigation strategy that improves dietary energy efficiency for growth and carcass mass deposition. Furthermore, thiamine increases heat losses through the body surface, regardless of gender. Full article
(This article belongs to the Special Issue Effects of Heat Stress on Animal Reproduction and Production)
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17 pages, 4026 KB  
Article
Integrated Whole-Transcriptome Analysis to Elucidate the Core Regulatory Network of circRNA Involved in Ovarian Development and Reproductive Capacity Differences in Sheep: circRNA2058-miR-9226-5p-MET Axis
by Bo Gu, Anqi Wang, Xinmiao Yu, Ying Li, Yao Cong and Huaizhi Jiang
Animals 2025, 15(21), 3077; https://doi.org/10.3390/ani15213077 - 23 Oct 2025
Viewed by 222
Abstract
(1) Background: This study aims to systematically identify key candidate genes and the regulatory networks governing ovarian development in sheep breeds with divergent fecundity. Focusing on elucidating the central regulatory roles of these factors during distinct ovarian developmental stages in highly prolific breeds, [...] Read more.
(1) Background: This study aims to systematically identify key candidate genes and the regulatory networks governing ovarian development in sheep breeds with divergent fecundity. Focusing on elucidating the central regulatory roles of these factors during distinct ovarian developmental stages in highly prolific breeds, the research seeks to reveal the mechanism by which multilevel regulatory networks synergistically determine ewe reproductive capacity. (2) Methods: This study utilized the ovaries from the low-fecundity sheep breed Ujumqin sheep, the high-fecundity breed small-tailed Han sheep, and various developmental stages of small-tailed Han sheep as research subjects. Through whole-transcriptome sequencing analysis, differentially expressed mRNAs(DEGs) and non-coding RNAs (ncRNAs) were screened, and a ceRNA regulatory network was constructed and subjected to bioinformatic analysis. The dual-luciferase reporter gene detection system was employed to validate the targeting relationships within the obtained key circRNA-miRNA-mRNA networks. Finally, qRT-PCR was used to verify the accuracy of the sequencing results. (3) Results: Our analysis constructed two distinct ceRNA networks: one from different fecundity groups (116 DECs, 46 DEMs, 82 DEGs) and another from different ovarian stages (186 DECs, 143 DEMs, 338 DEGs). Functional enrichment revealed key reproduction-related pathways, including Mitogen-Activated Protein Kinase(MAPK), Janus Kinase-Signal Transducer and Activator of Transcription(JAK-STAT), and WNT signaling in the fecundity comparison, and MAPK, Ras, WNT, Hippo signaling in the developmental stage comparison. Integrated analysis identified a core circRNA-miRNA-mRNA network, pinpointing circRNA2058-miR-9226-5p-MET as a central regulatory axis. The dual-luciferase assay confirmed that circRNA2058 acts as a sponge for miR-9226-5p, thereby mediating MET expression. qRT-PCR validation of randomly selected RNAs confirmed the sequencing reliability. (4) Conclusions: this study deciphers a synergistic regulatory network and identifies, for the first time, the pivotal circRNA2058-miR-9226-5p-MET ceRNA axis as an potential critical molecular switch driving follicular dominance in sheep. This discovery provides a molecular foundation for targeting core regulators of ovine reproductive efficiency and offers significant insights for innovative strategies in enhancing sheep reproduction. Full article
(This article belongs to the Section Small Ruminants)
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19 pages, 2740 KB  
Article
Genome-Wide SNP Analysis Reveals the Unique Genetic Diversity Represented by Fat-Tailed Coarse-Wooled Sheep Breeds of Kazakhstan
by Kairat Dossybayev, Makpal Amandykova, Daniya Ualiyeva, Tilek Kapassuly, Altynay Kozhakhmet, Elena Ciani, Bakytzhan Bekmanov and Rauan Amzeyev
Biology 2025, 14(11), 1478; https://doi.org/10.3390/biology14111478 - 23 Oct 2025
Viewed by 342
Abstract
Background: The fat-tailed coarse-wooled sheep breeds exhibit excellent reproductive performance, exceptional adaptability to pasture conditions, and high precocity, contributing to enhanced meat, fat, and wool productivity in sheep breeding. Despite the significant role of these sheep breeds in Kazakhstan’s livestock production, their genetics [...] Read more.
Background: The fat-tailed coarse-wooled sheep breeds exhibit excellent reproductive performance, exceptional adaptability to pasture conditions, and high precocity, contributing to enhanced meat, fat, and wool productivity in sheep breeding. Despite the significant role of these sheep breeds in Kazakhstan’s livestock production, their genetics remain poorly studied. This raises concerns about the potential loss of unique, breed-specific traits that could be important for the future development and resilience of Kazakh stan’s sheep farming sector. This study aimed to analyze genome-wide genotyping SNP data of local fat-tailed coarse-wooled sheep breeds (Kazakh fat-tailed coarse-wooled, Edilbay, and Gissar) to reveal their genetic diversity, breed characteristics, and phylogenetic relationships with worldwide domestic sheep breeds and wild sheep. Methods: The OvineSNP50 Genotyping BeadChip was used to obtain genome-wide SNP genotyping data from 160 fat-tailed coarse-wooled sheep from Kazakhstan. Population structure analysis, principal component analysis, phylogenetic and the maximum likelihood tree analysis were performed in comparison with foreign domestic sheep breeds and wild sheep populations. Results: Kazakh breeds exhibited high genetic diversity, with Edilbay showing the greatest allelic richness. PCA and Admixture revealed clear differentiation among the three breeds: Edilbay and Gissar formed homogeneous clusters, while Kazakh fat-tailed coarse-wooled sheep displayed admixture and substructure. Evidence of gene flow from Edilbay into other Kazakh populations supports its role as a genetic source for regional breeds. Phylogenetic analysis placed Kazakhstani sheep close to other Central Asian breeds, while clearly distinct from East Asian and European populations. Wild sheep (Argali and Urial) formed separate clades, with Kerman wild sheep clustering closer to Urial. Conclusions: Our results highlight the value of genotyping data for studying genetic diversity and population structure. Developing genetic resources for Kazakhstan’s native sheep breeds will help preserve their unique diversity and ensure it remains available for future use in breeding and adaptation efforts. Full article
(This article belongs to the Special Issue Genetic Variability within and between Populations)
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17 pages, 1703 KB  
Article
Whole-Genome Resequencing Identifies Candidate Genes for Tail Fat Deposition in Sheep
by Xiaowen Zhang, Yufei Li, Yongqing Zhao, Penghui Guo, Yong Cai, Hongwei Xu, Xin Cao, Qiongyi Li, Xiaoxia Ma, Derong Zhang and Jialin Bai
Animals 2025, 15(20), 3046; https://doi.org/10.3390/ani15203046 - 20 Oct 2025
Viewed by 366
Abstract
Excessive adipose tissue accumulation in sheep disrupts insulin signaling, inducing insulin resistance, and alters energy partitioning mechanisms. These changes adversely affect both ovine health and production efficiency. This study employed whole-genome resequencing to conduct selection signal analysis in long-fat-tailed (Lanzhou fat-tailed sheep) and [...] Read more.
Excessive adipose tissue accumulation in sheep disrupts insulin signaling, inducing insulin resistance, and alters energy partitioning mechanisms. These changes adversely affect both ovine health and production efficiency. This study employed whole-genome resequencing to conduct selection signal analysis in long-fat-tailed (Lanzhou fat-tailed sheep) and short-fat-tailed (Hu sheep) breeds, investigating the genetic basis underlying divergent lipid metabolism-related traits between these distinct tail phenotypes. Fifteen healthy adult individuals, each from long-fat-tailed (Lanzhou Large-tailed sheep) and short-fat-tailed (Hu sheep) breeds, underwent whole-genome resequencing. Whole-genome resequencing analyses via FST, XP-CLR, and XP-EHH identified 75 significantly selected regions (p < 0.01), revealing eight key candidate genes (DAB1, DPP10, EPHA6, GPC5, KLF12, PAK7, PTPN3, TENM3). Subsequent functional enrichment analysis demonstrated significant enrichment of DAB1 and GPC5 in lipid metabolic processes (GO:0006629). Employing whole-genome resequencing-based selection signal analysis in long-fat-tailed (Lanzhou Large-tailed sheep) and short-fat-tailed (Hu sheep) breeds, this study identified two key lipid metabolism-associated genes (DAB1 and GPC5). These findings provide critical insights for conserving genetic resources and informing molecular breeding strategies targeting divergent tail phenotypes. Full article
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22 pages, 4448 KB  
Article
Genome-Wide Association Study Revealed Candidate Genes Associated with Litter Size, Weight, and Body Size Traits in Tianmu Polytocous Sheep (Ovis aries)
by Wenna Liu, Shengchao Ma, Qingwei Lu, Sen Tang, Nuramina Mamat, Yaqian Wang, Wei Hong, Xiangrong Hu, Cuiling Wu and Xuefeng Fu
Biology 2025, 14(10), 1446; https://doi.org/10.3390/biology14101446 - 20 Oct 2025
Viewed by 455
Abstract
Reproductive and growth traits are key economic traits in sheep. This study aims to identify key single nucleotide polymorphisms (SNPs) and candidate genes associated with reproductive and growth traits in Tianmu polytocous sheep through a genome-wide association study (GWAS). The findings are expected [...] Read more.
Reproductive and growth traits are key economic traits in sheep. This study aims to identify key single nucleotide polymorphisms (SNPs) and candidate genes associated with reproductive and growth traits in Tianmu polytocous sheep through a genome-wide association study (GWAS). The findings are expected to provide both a theoretical foundation for molecular breeding in this breed and novel insights into the genetic basis of ovine reproductive and growth performance. This study took 483 adult Tianmu polytocous ewes as the research subjects, collected their lambing records, measured their phenotypic values of growth traits (3 weight and 11 body size traits), and collected their blood samples for whole-genome resequencing to identify SNPs in the Tianmu polytocous sheep genome. The results identified a total of 9,499,019 (3× coverage) and 27,413,216 (30× coverage) high-quality SNPs in the Tianmu polytocous sheep genome. Subsequently, the association analysis between SNPs and reproductive and growth traits was conducted using a mixed linear model. A total of 92, 66, 18, 28, 6, 42, 3, 3, 6, 1, 12, 3, 22, 8, 6, and 3 SNPs were found associated with litter size at first parity, litter size at second parity, litter size at third parity, litter size at fourth parity, birth weight, weaning weight, body height, withers height, body length, head length, head width, cannon bone circumference, forelimb height, chest girth, chest depth, and withers width, respectively. Further, based on SNP annotation, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, candidate genes associated with the reproductive and growth traits were identified. Among these genes, 11 LOC, DEPTOR, GNG12, GRM7, PTH, PTH2R, WWOX, INHA, and NRG3 are candidate genes associated with litter size at first parity or litter size at third parity. These genes are involved in the G protein-coupled receptor signaling pathway, G protein-coupled receptor activity, ovarian tissue development, and hormone secretion. Additionally, TFRC and NTN1 are candidate genes associated with birth weight, while five UGT1A and CASR are candidate genes associated with weaning weight. These candidate genes are primarily involved in lipid metabolism. Finally, the following genes were identified as candidates associated with specific traits: DLG2, TMEM126A, and TMEM126B with body height; DSCAM and SCN8A with body length; BARX1 with cannon bone circumference; four LOC genes with forelimb height; EPHA4 with chest depth; and MRS2 with withers width. Full article
(This article belongs to the Section Genetics and Genomics)
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14 pages, 2273 KB  
Case Report
Population Structure and Genetic Diversity of Tibetan Sheep Revealed by Whole-Genome Resequencing: Implications for Conservation and Breeding
by Junxia Zhang, Litan Zhang, Yuxiang Zhang, Yuting Deng and Xiaocheng Wen
Genes 2025, 16(10), 1232; https://doi.org/10.3390/genes16101232 - 18 Oct 2025
Viewed by 334
Abstract
Background: Tibetan sheep (Ovis aries) have evolved remarkable adaptations to the extreme high-altitude environment of the Qinghai–Tibet Plateau. While previous studies have identified some genetic features underlying these adaptations, a comprehensive understanding of their population genetics and selection signatures remains incomplete. [...] Read more.
Background: Tibetan sheep (Ovis aries) have evolved remarkable adaptations to the extreme high-altitude environment of the Qinghai–Tibet Plateau. While previous studies have identified some genetic features underlying these adaptations, a comprehensive understanding of their population genetics and selection signatures remains incomplete. We hypothesized that Tibetan sheep harbor unique genetic diversity and population structure distinct from low-altitude sheep (Hu sheep and Small Tail Han sheep), and that whole-genome resequencing could identify key positively selected genes driving their high-altitude adaptation and economic trait variation. Thus, this study aimed to characterize the population structure and genetic diversity of Tibetan sheep via whole-genome resequencing and identify genomic regions and candidate genes under positive selection related to high-altitude adaptation and important economic traits (growth, meat quality, wool, reproduction). Results: Using whole-genome resequencing of 90 Tibetan sheep (ZY) compared to 90 Hu sheep (HY) and 90 Small Tail Han sheep (XWHY), we identified significantly higher genetic diversity in Tibetan sheep (Pn = 0.6399, PIC = 0.1731). Population structure analyses revealed distinct clustering of Tibetan sheep, with principal components explaining 20.69% (PCA1), 12.26% (PCA2), and 14.18% (PCA3) of genetic variation. Selective sweep analysis identified 713 genomic regions (containing 207 genes) under positive selection, including key hypoxia adaptation genes (HDAC5, BMP2/BMPR1B, DUOX2) and economic trait genes (FGF9 for growth; SLC27A2 for meat quality; KRTAP for wool; IZUMO1R for reproduction). Functional enrichment highlighted pathways in oxygen transport (EPO regulation), energy metabolism (fatty acid β-oxidation), and vascular remodeling (TGF-β signaling). Conclusions: Our study provides the most comprehensive genomic characterization of Tibetan sheep to date, revealing both their unique genetic diversity and molecular mechanisms of high-altitude adaptation. The identified candidate genes offer valuable targets for marker-assisted breeding to improve productivity while maintaining adaptive traits, supporting sustainable development of plateau animal husbandry. Full article
(This article belongs to the Section Population and Evolutionary Genetics and Genomics)
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13 pages, 6103 KB  
Article
Regulatory of Oleuropein on the In Vitro Maturation of Oocytes and the Development of Parthenogenetic Embryos in Sheep
by Yue Zhang, Wenjuan Zhao, Zihao Ma, Zhenghang Li, Zhijiao Liu, Pengcheng Wan and Guangdong Hu
Animals 2025, 15(20), 3011; https://doi.org/10.3390/ani15203011 - 17 Oct 2025
Viewed by 342
Abstract
Oleuropein (OLE), as the main effective active component in olive leaves, is a natural cyclic ether terpene polyphenolic compound found in plants of the genus Olea. It has antioxidant, anti-inflammatory and anti-apoptotic properties, and can reduce damage caused by reactive oxygen species. These [...] Read more.
Oleuropein (OLE), as the main effective active component in olive leaves, is a natural cyclic ether terpene polyphenolic compound found in plants of the genus Olea. It has antioxidant, anti-inflammatory and anti-apoptotic properties, and can reduce damage caused by reactive oxygen species. These characteristics indicate that it can enhance the maturation rate of oocytes and the developmental capacity of embryos—two key indicators in animal breeding. This study evaluated the effects of OLE on the in vitro maturation and early embryonic development of sheep oocytes. 20 μM OLE has the best promoting effect on the maturation rate of oocytes, and 30 μM OLE has the best increasing effect on the blastocyst rate. Compared with the control group, glutathione (GSH) level and mitochondrial membrane potential (MMP) level were significantly increased, ROS level was significantly decreased, the expression of antioxidant genes SOD1 and GPX3 was significantly elevated, and the expression of anti-apoptotic gene BCL2 was significantly elevated in the experimental group. In addition, during the in vitro development stage of early embryos, the expression level of the embryo development-related gene OCT4 significantly increased. The study has shown that OLE can effectively alleviate oxidative stress during in vitro culture, increase oocyte maturation rate and promote embryo development. Full article
(This article belongs to the Section Animal Reproduction)
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16 pages, 9307 KB  
Article
Projected Heat-Stress in Sheep and Cattle in Greece Under Future Climate Change Scenarios
by Dimitris K. Papanastasiou, Athanasios I. Gelasakis, Giorgos Papadopoulos, Dimitrios Melas, Kostas Douvis, Ioannis Faraslis, Stavros Keppas, Ioannis Stergiou, Anastasia Poupkou, Dimitris Voloudakis, Athena Progiou, John Kapsomenakis and Nikolaos Katsoulas
Agriculture 2025, 15(20), 2141; https://doi.org/10.3390/agriculture15202141 - 15 Oct 2025
Viewed by 395
Abstract
It is well established that exposure to heat-stress conditions significantly impacts the physiology, health, welfare, and productivity of both sheep and cattle. The aim of this study was to apply the Temperature Humidity Index (THI) in order to assess the impact of future [...] Read more.
It is well established that exposure to heat-stress conditions significantly impacts the physiology, health, welfare, and productivity of both sheep and cattle. The aim of this study was to apply the Temperature Humidity Index (THI) in order to assess the impact of future climate conditions on the thermal stress exposure of sheep and cattle in Greece. The Weather Research and Forecasting (WRF) model was used as a high-resolution regional climate model to simulate climate conditions for two decades in Greece at a 10 Km spatial resolution and a 1 h temporal resolution. The WRF model was applied to two emission scenarios, namely SSP2-4.5 (intermediate) and SSP5-8.5 (worst-case). Projections were made for the near-future decade (2046–2055), with the decade (2005–2014) serving as the reference period for comparative analysis. The data analysis indicated that under the SSP2-4.5 emission scenario, the mean temperature is projected to increase by 1.2–1.4 °C and 1.4–1.6 °C across 38% and 58% of the country’s territory, respectively. Increases higher than 1.6 °C are projected across 32% of the Greek territory under the SSP5-8.5 emission scenario. The mean THI (sheep) and mean THI (adj) (cattle) are projected to increase by 5–10% and by 4% across 74% and 82% of the Greek territory, respectively, when considering the SSP2-4.5 emission scenario. Slightly more severe mean heat-stress conditions were projected when considering the SSP5-8.5 emission scenario. The analysis of the hourly THI values showed that sheep and cattle are expected to experience heat-stress conditions during extended periods in the future, in which hot weather will prevail. Specifically, the number of severe/danger heat-stress hours is projected to double in the greater part of the country. To mitigate the adverse effects of climate-change-induced thermal stress on animal productivity, health, and welfare, the implementation of adaptation measures and best management practices is strongly recommended for sheep and cattle farmers. These measures encompass improvements in breeding strategies, livestock housing and microclimate management, nutritional interventions, and the adoption of precision livestock farming technologies. Given the outstanding economic, social, and environmental importance of sheep and cattle farming in Greece, effective adaptation to and mitigation of climate change impacts represent urgent priorities to ensure the long-term sustainability and resilience of the livestock sector. Full article
(This article belongs to the Special Issue The Threats Posed by Environmental Factors to Farm Animals)
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17 pages, 2431 KB  
Article
Genetic Diversity and Population Structure of Fat-Tailed Coarse-Wooled Sheep Breeds Ovis aries from Kazakhstan
by Kairat Dossybayev, Daniya Ualiyeva, Tilek Kapassuly, Makpal Amandykova, Altynay Kozhahmet, Bakytzhan Bekmanov, Rauan Amzeyev and Saitou Naruya
Vet. Sci. 2025, 12(10), 988; https://doi.org/10.3390/vetsci12100988 - 13 Oct 2025
Viewed by 554
Abstract
Sheep play a central role in Kazakhstan’s pastoral economy, yet the maternal genetic composition of its traditional breeds remains poorly characterized. We analyzed partial mitochondrial D-loop sequences (848 bp) from 115 individuals of three fat-tailed coarse-wooled breeds (Edilbay, Kazakh fat-tailed coarse-wooled, and Gissar) [...] Read more.
Sheep play a central role in Kazakhstan’s pastoral economy, yet the maternal genetic composition of its traditional breeds remains poorly characterized. We analyzed partial mitochondrial D-loop sequences (848 bp) from 115 individuals of three fat-tailed coarse-wooled breeds (Edilbay, Kazakh fat-tailed coarse-wooled, and Gissar) to assess genetic diversity, population structure, and phylogenetic relationships. Ninety-eight haplotypes were identified, indicating high haplotype diversity (Hd = 0.996 ± 0.002) and moderate nucleotide diversity (π = 0.02624 ± 0.00048). Haplotypes clustered into haplogroups A (57.4%) and B (42.6%), with Edilbay dominating the star-like cluster of haplogroup A, consistent with recent expansion. AMOVA revealed that most variation (92.03%) occurred within populations, with no significant differentiation among breeds. Phylogenetic analyses placed Edilbay close to the most recent common ancestor of fat-tailed domestic sheep and the wild Ovis species, suggesting retention of an ancestral lineage. These findings highlight Kazakhstan as a genetic crossroads in sheep history and underscore the conservation value of its maternal diversity. Full article
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17 pages, 2727 KB  
Article
Novel Silent Mutations in the HIRA Gene Associated with Litter Size in Sonid Sheep
by Chen Wang, Zhana Naren, He Bu, Ming Cang, Guifang Cao, Buhe Nashun and Bin Tong
Animals 2025, 15(20), 2936; https://doi.org/10.3390/ani15202936 - 10 Oct 2025
Viewed by 374
Abstract
Improving ovine reproductive efficiency is an important breeding goal that could substantially enhance economic viability in the sheep industry. The histone cell cycle regulator (HIRA) gene has been functionally validated as a reproductive regulator in model organisms such as Drosophila and [...] Read more.
Improving ovine reproductive efficiency is an important breeding goal that could substantially enhance economic viability in the sheep industry. The histone cell cycle regulator (HIRA) gene has been functionally validated as a reproductive regulator in model organisms such as Drosophila and murine species; however, research on the effects of HIRA on the prolificacy in sheep remains scarce. Thus, this study aimed to investigate the association between genetic variants of HIRA and litter size in sheep. In brief, we identified 15 novel exonic mutations in the Sonid sheep breed via direct sequencing. Notably, a linkage disequilibrium including the c.1521C>G, c.1572C>T, and c.1578G>A mutations on exon 14 of HIRA exhibited a significant association with litter size in Sonid sheep (p < 0.01). Meanwhile, it was predicted that mutations play a major role in enhancing the stability of the mRNA secondary structure by lowering the minimum free energy, and mutations were also thought to change the mRNA secondary structure of ovine HIRA. Therefore, these findings may provide potentially useful molecular markers for optimizing reproductive performance in Sonid sheep. Full article
(This article belongs to the Section Animal Reproduction)
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