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14 pages, 1365 KiB  
Article
Molecular Genetic Basis of Reproductive Fitness in Tibetan Sheep on the Qinghai-Tibet Plateau
by Wangshan Zheng, Siyu Ge, Zehui Zhang, Ying Li, Yuxing Li, Yan Leng, Yiming Wang, Xiaohu Kang and Xinrong Wang
Genes 2025, 16(8), 909; https://doi.org/10.3390/genes16080909 - 29 Jul 2025
Viewed by 79
Abstract
Background: Complete environmental adaptation requires both survival and reproductive success. The hypoxic Qinghai-Tibet Plateau (>3000 m) challenges reproduction in indigenous species. Tibetan sheep, a key plateau-adapted breed, possess remarkable hypoxic tolerance, yet the genetic basis of their reproductive success remains poorly understood. [...] Read more.
Background: Complete environmental adaptation requires both survival and reproductive success. The hypoxic Qinghai-Tibet Plateau (>3000 m) challenges reproduction in indigenous species. Tibetan sheep, a key plateau-adapted breed, possess remarkable hypoxic tolerance, yet the genetic basis of their reproductive success remains poorly understood. Methods: We integrated transcriptomic and genomic data from Tibetan sheep and two lowland breeds (Small-tailed Han sheep and Hu sheep) to identify Tibetan sheep reproduction-associated genes (TSRGs). Results: We identified 165 TSRGs: four genes were differentially expressed (DEGs) versus Small-tailed Han sheep, 77 DEGs versus Hu sheep were found, and 73 genes were annotated in reproductive pathways. Functional analyses revealed enrichment for spermatogenesis, embryonic development, and transcriptional regulation. Notably, three top-ranked selection signals (VEPH1, HBB, and MEIKIN) showed differential expression. Murine Gene Informatics (MGI) confirmed that knockout orthologs exhibit significant phenotypes including male infertility, abnormal meiosis (male/female), oligozoospermia, and reduced neonatal weight. Conclusions: Tibetan sheep utilize an evolved suite of genes underpinning gametogenesis and embryogenesis under chronic hypoxia, ensuring high reproductive fitness—a vital component of their adaptation to plateaus. These genes provide valuable genetic markers for the selection, breeding, and conservation of Tibetan sheep as a critical genetic resource. Full article
(This article belongs to the Section Animal Genetics and Genomics)
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20 pages, 1256 KiB  
Review
Exploring Meiotic Recombination and Its Potential Benefits in South African Beef Cattle: A Review
by Nozipho A. Magagula, Keabetswe T. Ncube, Avhashoni A. Zwane and Bohani Mtileni
Vet. Sci. 2025, 12(7), 669; https://doi.org/10.3390/vetsci12070669 - 16 Jul 2025
Viewed by 439
Abstract
Meiotic recombination is a key evolutionary process that generates novel allele combinations during prophase I of meiosis, promoting genetic diversity and enabling the selection of desirable traits in livestock breeding. Although its molecular mechanisms are well-characterised in model organisms such as humans and [...] Read more.
Meiotic recombination is a key evolutionary process that generates novel allele combinations during prophase I of meiosis, promoting genetic diversity and enabling the selection of desirable traits in livestock breeding. Although its molecular mechanisms are well-characterised in model organisms such as humans and mice, studies in African indigenous cattle, particularly South African breeds, remain scarce. Key regulators of recombination, including PRDM9, SPO11, and DMC1, play essential roles in crossover formation and genome stability, with mutations in these genes often linked to fertility defects. Despite the Bonsmara and Nguni breeds’ exceptional adaptability to arid and resource-limited environments, little is known about how recombination contributes to their unique genetic architecture and adaptive traits. This review synthesises the current knowledge on the molecular basis of meiotic recombination, with a focus on prophase I events and associated structural proteins and enzymes. It also highlights the utility of genome-wide tools, particularly high-density single nucleotide polymorphism (SNP) markers for recombination mapping. By focusing on the underexplored recombination landscape in South African beef cattle, this review identifies key knowledge gaps. It outlines how recombination studies can inform breeding strategies aimed at enhancing genetic improvement, conservation, and the long-term sustainability of local beef production systems. Full article
(This article belongs to the Section Veterinary Biomedical Sciences)
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13 pages, 3548 KiB  
Article
Analysis of Carcass and Meat Characteristics in Breast Muscle Between Hubbard White Broilers and Xueshan Chickens
by Fan Li, Xingyu Zhang, Jiajia Yu, Jiaxue Yuan, Yuanfeng Zhang, Huiting He, Qing Ma, Yinglin Lu, Xiaoe Xiang and Minli Yu
Animals 2025, 15(14), 2099; https://doi.org/10.3390/ani15142099 - 16 Jul 2025
Viewed by 296
Abstract
The focus on selecting broilers for rapid growth rates and enhanced breast muscle yield has resulted in a decline in meat quality. The differences in carcass characteristics and meat quality between Hubbard white broilers (HWs, a commercial breed) and Xueshan chickens (XSs, an [...] Read more.
The focus on selecting broilers for rapid growth rates and enhanced breast muscle yield has resulted in a decline in meat quality. The differences in carcass characteristics and meat quality between Hubbard white broilers (HWs, a commercial breed) and Xueshan chickens (XSs, an indigenous breed) at market age were analyzed to determine the potential mechanisms responsible for these differences. The results show that HWs exhibited significantly better carcass performance than XSs, including the larger weight of the carcass, the breast muscle, and the thigh muscle (p < 0.01). In addition, based on HE staining analysis, HWs’ breast muscles had a considerably larger average myofiber area and diameter than those of XSs (p < 0.01). Furthermore, the physical characteristics of the meat revealed that XSs had higher redness and yellowness and also higher lightness. HW meat had a higher pH and thermal loss, but a lower shear force and drip loss than XS meat (p < 0.01). The content of saturated fatty acids (SFAs) and polyunsaturated fatty acids (PUFAs) was, remarkably, lower in the breast muscles of HWs than of XSs (p < 0.01). In contrast, HWs had a larger concentration of monounsaturated fatty acids (MUFAs) than XSs (p < 0.01). Finally, the breast muscles of XSs had lower levels of mRNA expression for genes linked to lipid metabolism, such as fatty acid binding protein 4 (Fabp4) and peroxisome proliferator-activated receptor alpha (Pparα), and had higher levels of the phosphofructokinase muscle type (Pfkm) compared to HWs (p < 0.01). These results indicate that a lower carcass yield was observed in XSs compared with HWs, but that XSs showed better performance in terms of meat quality than HW. Full article
(This article belongs to the Special Issue Advances in Genetic Analysis of Important Traits in Poultry)
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12 pages, 2564 KiB  
Article
Genetic Diversity and Population Structure Analysis of Luhua chickens Based on Genome-Wide Markers
by Qianwen Yang, Wei Han, Jun Yan, Chenghao Zhou, Guohui Li, Huiyong Zhang, Jianmei Yin and Xubin Lu
Animals 2025, 15(14), 2071; https://doi.org/10.3390/ani15142071 - 14 Jul 2025
Viewed by 240
Abstract
The Luhua chicken is an outstanding local breed in China that has been placed under conservation due to the impact of specialized breeding and the widespread adoption of commercial varieties. As such, this study analyzed reproductive traits across three consecutive generations and utilized [...] Read more.
The Luhua chicken is an outstanding local breed in China that has been placed under conservation due to the impact of specialized breeding and the widespread adoption of commercial varieties. As such, this study analyzed reproductive traits across three consecutive generations and utilized whole-genome resequencing data from 60 Luhua chickens to assess conservation efficacy through genetic diversity, run of homozygosity (ROH) distribution, kinship, and population structure so as to better conserve the breed. The results show that, across generations, the body weight at first egg increased, the age at first egg was delayed, and the egg weight at first laying increased. No significant variations were found in the body weight at 300 d or the total egg number. The key genetic parameters of the polymorphism information content (PIC), expected heterozygosity (HE), observed heterozygosity (HO), and mean identical-by-state (IBS) distance were 0.234, 0.351, 0.277, and 0.782, respectively. The majority of ROHs ranged from 0.5 to 1 Mb, and the inbreeding coefficient based on ROHs was calculated at 0.021. The findings reveal that these traits remained unchanged across the three generations. Our research suggests that optimizing the mating plan of Luhua chickens is essential to minimize inbreeding risk. Furthermore, the methodology applied in this study provides a valuable reference for the conservation monitoring of other indigenous chicken breeds. Full article
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18 pages, 3983 KiB  
Article
Prediction of Mature Body Weight of Indigenous Camel (Camelus dromedarius) Breeds of Pakistan Using Data Mining Methods
by Daniel Zaborski, Wilhelm Grzesiak, Abdul Fatih, Asim Faraz, Mohammad Masood Tariq, Irfan Shahzad Sheikh, Abdul Waheed, Asad Ullah, Illahi Bakhsh Marghazani, Muhammad Zahid Mustafa, Cem Tırınk, Senol Celik, Olha Stadnytska and Oleh Klym
Animals 2025, 15(14), 2051; https://doi.org/10.3390/ani15142051 - 11 Jul 2025
Viewed by 358
Abstract
The determination of the live body weight of camels (required for their successful breeding) is a rather difficult task due to the problems with handling and restraining these animals. Therefore, the main aim of this study was to predict the ABW of eight [...] Read more.
The determination of the live body weight of camels (required for their successful breeding) is a rather difficult task due to the problems with handling and restraining these animals. Therefore, the main aim of this study was to predict the ABW of eight indigenous camel (Camelus dromedarius) breeds of Pakistan (Bravhi, Kachi, Kharani, Kohi, Lassi, Makrani, Pishin, and Rodbari). Selected productive (hair production, milk yield per lactation, and lactation length) and reproductive (age of puberty, age at first breeding, gestation period, dry period, and calving interval) traits served as the predictors. Six data mining methods [classification and regression trees (CARTs), chi-square automatic interaction detector (CHAID), exhaustive CHAID (EXCHAID), multivariate adaptive regression splines (MARSs), MLP, and RBF] were applied for ABW prediction. Additionally, hierarchical cluster analysis with Euclidean distance was performed for the phenotypic characterization of the camel breeds. The highest Pearson correlation coefficient between the observed and predicted values (0.84, p < 0.05) was obtained for MLP, which was also characterized by the lowest root-mean-square error (RMSE) (20.86 kg), standard deviation ratio (SDratio) (0.54), mean absolute percentage error (MAPE) (2.44%), and mean absolute deviation (MAD) (16.45 kg). The most influential predictor for all the models was the camel breed. The applied methods allowed for the moderately accurate prediction of ABW (average R2 equal to 65.0%) and the identification of the most important productive and reproductive traits affecting its value. However, one important limitation of the present study is its relatively small dataset, especially for training the ANN (MLP and RBF). Hence, the obtained preliminary results should be validated on larger datasets in the future. Full article
(This article belongs to the Section Animal System and Management)
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16 pages, 4159 KiB  
Article
Integrated Transcriptomic and Metabolic Analyses Highlight Key Pathways Involved in the Somatic Embryogenesis of Picea mongolica
by Jinling Dai, Shengli Zhang and Yu’e Bai
Plants 2025, 14(14), 2141; https://doi.org/10.3390/plants14142141 - 11 Jul 2025
Viewed by 357
Abstract
In the severe environment of Hunshandake Sandy Land, the uncommon and indigenous Chinese tree species Picea mongolica is an important biological component. Conventional seed propagation in P. mongolica is constrained by low germination rates, prolonged breeding cycles, and hybrid offspring genetic instability, limiting [...] Read more.
In the severe environment of Hunshandake Sandy Land, the uncommon and indigenous Chinese tree species Picea mongolica is an important biological component. Conventional seed propagation in P. mongolica is constrained by low germination rates, prolonged breeding cycles, and hybrid offspring genetic instability, limiting efficient varietal improvement. In contrast, somatic embryogenesis (SE) offers superior propagation efficiency, exceptional germination synchrony, and strict genetic fidelity, enabling rapid mass production of elite regenerants. However, SE in P. mongolica is hampered by severe genotype dependence, poor mature embryo induction rates, and loss of embryogenic potential during long-term cultures, restricting the production of high-quality seedlings. In this study, we aimed to analyze the transcriptome and metabolome of three crucial phases of SE: mature somatic embryos (MSEs), globular somatic embryos (GSEs), and embryogenic calli (EC). Numerous differentially expressed genes (DEGs) were found, especially in pathways linked to ribosomal functions, flavonoid biosynthesis, and the metabolism of starch and sucrose. Additionally, 141 differentially accumulated metabolites (DAMs) belonging to flavonoids, organic acids, carbohydrates, lipids, amino acids, and other metabolites were identified. An integrated study of metabolomic and transcriptome data indicated considerable enrichment of DEGs and DAMs in starch and sucrose metabolism, as well as phenylpropanoid biosynthesis pathways, all of which are required for somatic embryo start and development. This study revealed a number of metabolites and genes linked with SE, offering important insights into the molecular mechanisms driving SE in P. mongolica and laying the groundwork for the development of an efficient SE system. Full article
(This article belongs to the Section Plant Physiology and Metabolism)
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22 pages, 2749 KiB  
Article
Genetic Diversity, Population Structure, and Historical Gene Flow Patterns of Nine Indigenous Greek Sheep Breeds
by Sofia Michailidou, Maria Kyritsi, Eleftherios Pavlou, Antiopi Tsoureki and Anagnostis Argiriou
Biology 2025, 14(7), 845; https://doi.org/10.3390/biology14070845 - 10 Jul 2025
Viewed by 414
Abstract
Ιn this study, we evaluated the genetic resources of nine Greek sheep breeds. The genotyping data of 292 animals were acquired from Illumina’s OvineSNP50 Genotyping BeadChip. The genetic diversity and inbreeding levels were evaluated using the observed and expected heterozygosity indices, the F [...] Read more.
Ιn this study, we evaluated the genetic resources of nine Greek sheep breeds. The genotyping data of 292 animals were acquired from Illumina’s OvineSNP50 Genotyping BeadChip. The genetic diversity and inbreeding levels were evaluated using the observed and expected heterozygosity indices, the FIS inbreeding coefficient, and runs of homozygosity (ROH). The genetic differentiation of breeds was assessed using the FST index, whereas their population structure was analyzed using admixture and principal components analysis (PCA). Historical recombination patterns and genetic drift were evaluated based on linkage disequilibrium, effective population sizes, and gene flow analysis to reveal migration patterns. PCA revealed distinct clusters mostly separating mountainous, insular, and lowland breeds. The FST value was the lowest between Serres and Karagouniko breeds (0.050). Admixture analysis revealed a genetic substructure for Serres and Kalarritiko breeds, while Chios, followed by Katsika, demonstrated the highest within-breed genetic uniformity. ROH analysis revealed low levels of inbreeding for all breeds. Genetic introgression from both Anatolia and Eastern Europe has been evidenced for Greek sheep breeds. The results also revealed that Greek sheep breeds maintain adequate levels of genetic diversity, without signs of excessive inbreeding, and can serve as valuable resources for the conservation of local biodiversity. Full article
(This article belongs to the Special Issue Genetic Variability within and between Populations)
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13 pages, 3693 KiB  
Article
Mapping of a Novel Quantitative Trait Locus Conferring Bacterial Blight Resistance in the Indigenous Upland Rice Variety ULR207 Using the QTL–Seq Approach
by Tanawat Wongsa, Sompong Chankaew, Tidarat Monkham, Meechai Siangliw, Niranjan Baisakh and Jirawat Sanitchon
Plants 2025, 14(14), 2113; https://doi.org/10.3390/plants14142113 - 9 Jul 2025
Viewed by 358
Abstract
Bacterial blight (BB) disease is a serious stress that affects up to 80% of rice yield. Utilizing an elite resistant variety was previously thought to be an alternative way to control disease outbreaks. The indigenous upland rice variety ULR207 is a high-potential donor [...] Read more.
Bacterial blight (BB) disease is a serious stress that affects up to 80% of rice yield. Utilizing an elite resistant variety was previously thought to be an alternative way to control disease outbreaks. The indigenous upland rice variety ULR207 is a high-potential donor for the BB resistance breeding program. However, the quantitative trait loci (QTLs) associated with bacterial blight resistance in this variety have not yet been discovered. Therefore, QTLs associated with BB resistance need to be identified. In this study, we identified the QTLs associated with BB resistance in the F2:3 population crossed between the BB resistance variety ULR207 and Maled Phai, as well as a susceptible variety, via QTL-seq analysis and bulk-segregant analysis. We found a new QTL-associated BB resistance locus (qBBchr8) mapped on chromosome 8. Five positions were candidates, including Os08g0110700, Os08g0115200, Os08g0131300, Os08g0139500, and Os08g0163900. Afterwards, Kompetitive Allele-Specific PCR (KASP) markers specific to the SNP variant and the position of each gene were designed. These markers, associated with the disease lesion length phenotype, were validated with another 178 individual plants of the F2 population via single-marker analysis. This analysis revealed that the position Os08g0110700 was the strongest locus, with a PVE of 15.00%. The results suggest that this KASP SNP marker could be used to improve elite rice for BB resistance. Full article
(This article belongs to the Special Issue Rice Genetics and Molecular Design Breeding)
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20 pages, 1908 KiB  
Article
Effects of Dietary Calcium and Phosphorus Levels on Growth Performance, Calcium–Phosphorus Homeostasis, and Gut Microbiota in Ningxiang Pigs
by Wenzhi Liu, Cheng Zhang, Xijie Kuang, Xianglin Zeng, Jiaqi Zhang, Qiye Wang and Huansheng Yang
Life 2025, 15(7), 1083; https://doi.org/10.3390/life15071083 - 9 Jul 2025
Viewed by 357
Abstract
Optimal dietary calcium (Ca) and phosphorus (P) requirements remain undetermined for Ningxiang pigs, a valuable indigenous Chinese breed. This study conducted a continuous feeding trial with two growth phases (grower: 30–50 kg; finisher: 50–80 kg) using fixed Ca/P ratios to systematically evaluate the [...] Read more.
Optimal dietary calcium (Ca) and phosphorus (P) requirements remain undetermined for Ningxiang pigs, a valuable indigenous Chinese breed. This study conducted a continuous feeding trial with two growth phases (grower: 30–50 kg; finisher: 50–80 kg) using fixed Ca/P ratios to systematically evaluate the effects of Ca/P levels on growth performance and mineral metabolism. A total of 180 pigs per phase were allocated to four Ca/P levels. During the grower phase, a dietary regimen of 0.83% Ca/0.67% P significantly increased the average daily feed intake (ADFI), average daily gain (ADG), and apparent total tract digestibility (ATTD) of energy and P. In the finisher phase, 0.60/0.48% Ca/P showed optimal growth performance, upregulated jejunal mineral transporters (CaSR and SLC34A2), enhanced bone mineralization (metatarsal ash content), and improved intestinal morphology (duodenal and jejunal villus height, jejunal villus surface area). This regimen also selectively enriched Peptostreptococcaceae abundance, indicating improved host–microbe interactions. Based on these findings, stage-specific nutritional strategies were recommended: 0.83% Ca/0.67% P during the grower phase and 0.60% Ca/0.48% P during the finisher phase. These protocols synergistically improve microbial ecology, intestinal function, and bone metabolism, thereby maximizing the growth potential of Ningxiang pigs. Full article
(This article belongs to the Special Issue Pig Microbiota Metabolism and Intestinal Health)
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17 pages, 4748 KiB  
Article
Impact of the Gut Microbiota–Metabolite Axis on Intestinal Fatty Acid Absorption in Huainan Pigs
by Jing Wang, Liangying Zhu, Yangyang Wang, Qiang Ma, Xiangzhou Yan, Mingxun Li and Baosong Xing
Microorganisms 2025, 13(7), 1609; https://doi.org/10.3390/microorganisms13071609 - 8 Jul 2025
Viewed by 433
Abstract
The gut microbiota critically influences lipid metabolism and fat deposition in pigs, processes that underpin pork quality preferences and differentiate the meat traits of Chinese indigenous breeds (fat-type) from those of Western commercial breeds (lean-type). To explore the mechanisms underlying breed-specific fatty acid [...] Read more.
The gut microbiota critically influences lipid metabolism and fat deposition in pigs, processes that underpin pork quality preferences and differentiate the meat traits of Chinese indigenous breeds (fat-type) from those of Western commercial breeds (lean-type). To explore the mechanisms underlying breed-specific fatty acid absorption, we compared the rectal and colonic microbiota and metabolite profiles of Huainan and Large White pigs using 16S rRNA sequencing and untargeted metabolomics. HN pigs exhibited enriched Lactobacillus johnsonii and Lactobacillus amylovorus, along with a significantly higher Firmicutes/Bacteroidetes ratio. Functional predictions further revealed elevated microbial pathways related to glycolysis, pyruvate metabolism, and ABC transporters in HN pigs. Conversely, LW pigs showed increased abundance of potentially pro-inflammatory bacteria and enriched pathways for lipopolysaccharide (LPS) biosynthesis. Metabolites such as 4-ethyl-2-heptylthiazole and picolinic acid were significantly upregulated in HN pigs and served as robust biomarkers (Area Under the Curve, AUC = 1.0),with perfect discrimination observed in both rectal and colonic samples. Integrative analysis identified 52 co-enriched microbial and metabolic pathways in HN pigs, including short-chain fatty acid (SCFA) production, lipid biosynthesis and transport, amino acid metabolism, ABC transporter activity, and the PPAR signaling pathway, supporting a microbiota–metabolite axis that enhances fatty acid absorption and gut immune balance. These findings provide mechanistic insight into breed-specific fat deposition and offer candidate biomarkers for improving pork quality via precision nutrition and breeding. Full article
(This article belongs to the Section Veterinary Microbiology)
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13 pages, 2083 KiB  
Article
Gut Fungal Community Modulates Fat Deposition in Ningxiang Pigs: Species-Specific Regulation via the Glucose–SCFAs Metabolic Axis
by Pengfei Huang, Hanmin Wang, Juan Wang, Zhenrong Qiu, Chunfeng Wang, Han Liu, Qiye Wang, Yali Li and Huansheng Yang
Animals 2025, 15(13), 1887; https://doi.org/10.3390/ani15131887 - 26 Jun 2025
Viewed by 289
Abstract
Despite limited understanding of gut fungal roles in fat deposition among indigenous pig breeds, a comparative study between high-fat-accumulating Ningxiang (NX) pigs and lean-type Duroc × Landrace × Yorkshire (DLY) pigs reveals a fungal-driven regulatory mechanism. NX pigs exhibited significantly higher fat percentage, [...] Read more.
Despite limited understanding of gut fungal roles in fat deposition among indigenous pig breeds, a comparative study between high-fat-accumulating Ningxiang (NX) pigs and lean-type Duroc × Landrace × Yorkshire (DLY) pigs reveals a fungal-driven regulatory mechanism. NX pigs exhibited significantly higher fat percentage, elevated serum glucose, and markedly reduced total colonic short-chain fatty acids (SCFAs) compared to DLY pigs (all p < 0.001), with butyrate showing the most pronounced decrease. Beta-diversity confirmed distinct fungal communities (p = 0.002), where NX pigs were enriched with Aspergillus and Penicillium, while DLY pigs harbored dominant Rhodotorula. Strong correlations were observed: NX-enriched fungi positively correlated with glucose and negatively with SCFAs, whereas Rhodotorula strongly associated with SCFAs (p < 0.001). FUNGuild analysis linked Aspergillus/Penicillium to enhanced polysaccharide degradation and glucose bioavailability. The findings propose a gut fungal-mediated “Glucose–SCFAs axis”: NX-enriched fungi elevate glucose (promoting lipogenesis) and suppress SCFAs (reducing butyrate-mediated adipocyte inhibition), whereas Rhodotorula in DLY pigs enhances SCFAs-induced lipolysis. Crucially, we demonstrate that fungal modulation primarily drives fat deposition differences between breeds, offering novel probiotics/antifungal strategies for precision swine breeding. Full article
(This article belongs to the Special Issue Advances in Pig Microbiome: Gut Influences and Beyond)
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21 pages, 2878 KiB  
Article
Genomic Analysis of Adaptability and Genetic Structure of Jabal Akhdar Goats: Evidence of Positive Selection in an Indigenous Omani Breed
by Zainab Mohammad, Hussain Bahbahani, Ahmad Alfoudari, Kaadhia Al Kharousi, Al Abeer Al Hamrashdi, Al Ghalya Al Toobi and Mohammad Al Abri
Biology 2025, 14(7), 761; https://doi.org/10.3390/biology14070761 - 25 Jun 2025
Viewed by 398
Abstract
Jabal Akhdar goats, native to Oman’s high-altitude Jabal Akhdar mountain range, are recognized for their high growth rate, remarkable twinning rate, and adaptability to harsh environmental conditions. This study assesses the genetic structure, inbreeding levels, effective population size (Ne), and [...] Read more.
Jabal Akhdar goats, native to Oman’s high-altitude Jabal Akhdar mountain range, are recognized for their high growth rate, remarkable twinning rate, and adaptability to harsh environmental conditions. This study assesses the genetic structure, inbreeding levels, effective population size (Ne), and linkage disequilibrium (LD) of Jabal Akhdar goats while identifying genomic regions under positive selection that may contribute to their environmental adaptation. The SNP genotypes from 72 Jabal Akhdar goats and two desert breeds from Egypt (153 Barki and 60 Saidi) revealed a clear genetic distinction between both groups. Within the Jabal Akhdar goats, genetic differentiation was also identified among the three sampled villages, indicating a village-specific genetic structure. The Jabal Akhdar breed exhibited a moderate level of inbreeding (FROH = 0.16), greater than that of the Barki and Saidi breeds. Additionally, Jabal Akhdar goats displayed greater LD and lower Ne levels compared to the Egyptian breeds. Analysis of runs of homozygosity (ROH) and extended haplotype homozygosity-based statistics (iHS and Rsb) identified 93 genomic regions exhibiting signatures of positive selection (80 from ROH, 5 from iHS, and 8 from Rsb). These regions harbor genes associated with traits essential for environmental adaptability, including hypoxia tolerance (SUCNR1, ANGPTL1, MITF, MTUS2), muscle development and function (MBNL1, ACTC1, CAPN5), fertility (GNRHR, CCNA1, SPAG1), UV radiation resistance (UVRAG, BRCA1), bone development (SOST, MEOX1), and lipid metabolism for energy utilization (DGAT2, G6PC, SUCLG2). The results of this study provide valuable insights for identifying causative variants and haplotypes underlying the Jabal Akhdar goat’s superior adaptability. These findings can guide breeders in designing conservation strategies and improving the productivity of this unique indigenous breed. Full article
(This article belongs to the Section Genetics and Genomics)
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17 pages, 2895 KiB  
Article
Whole-Transcriptome Sequencing and Differential Expression Analysis of the Epididymis in Junggar Bactrian Camels Before and After Sexual Maturity
by Jiahao Liu, Xinkui Yao, Jun Meng, Jianwen Wang, Yaqi Zeng, Linling Li and Wanlu Ren
Biology 2025, 14(7), 760; https://doi.org/10.3390/biology14070760 - 25 Jun 2025
Viewed by 359
Abstract
The Junggar Bactrian camel, a primitive indigenous breed in China, exhibits low reproductive efficiency under natural grazing conditions. This is partly attributed to the development of the epididymis and the quality of semen, both of which directly affect reproductive performance. The epididymis is [...] Read more.
The Junggar Bactrian camel, a primitive indigenous breed in China, exhibits low reproductive efficiency under natural grazing conditions. This is partly attributed to the development of the epididymis and the quality of semen, both of which directly affect reproductive performance. The epididymis is a key male reproductive organ responsible for sperm storage and transport. However, the gene expression profile of camel epididymal tissue remains poorly understood. In this study, we conducted whole-transcriptome sequencing of epididymal tissues from Junggar Bactrian camels before and after sexual maturity. A total of 683 differentially expressed mRNAs (DEmRNAs) were identified, including TPM2, ITGA5, FASN, and ACP5, of which 415 were upregulated and 268 were downregulated. Additionally, 260 differentially expressed long non-coding RNAs (DELncRNAs), including LOC123611838, LOC105083505, and LOC123614702, were identified, with 113 upregulated and 147 downregulated. An additional 11 differentially expressed microRNAs (DEmiRNAs), including eca-miR-206 and eca-miR-216a, were also detected. Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses revealed that key differentially expressed genes (DEGs), including TPM2, ITGA5, DDIT4, FASN, and ACP5, were mainly involved in pathways such as Cell Adhesion Molecules, Phospholipase D signaling, Cytokine–Cytokine Receptor Interaction, and Olfactory Transduction. This study presents a comprehensive whole-transcriptome analysis of the epididymis in Junggar Bactrian camels before and after sexual maturity, identifying key genes and regulatory pathways associated with epididymal development and reproductive function. These findings provide a theoretical foundation and valuable data for future research on reproductive performance and epididymal biology in Bactrian camels. Full article
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14 pages, 3201 KiB  
Article
Transcriptome Profiling Reveals Genetic Basis of Muscle Development and Meat Quality Traits in Chinese Congjiang Xiang and Landrace Pigs
by Jiada Yang, Qiaowen Tang, Chunying Sun, Qiuyue Li, Xiaoyu Li, Lu Hou, Yi Yang and Kang Yang
Metabolites 2025, 15(7), 426; https://doi.org/10.3390/metabo15070426 - 22 Jun 2025
Viewed by 389
Abstract
(1) Objectives: Understanding the genetic basis of muscle development and meat quality traits in divergent pig breeds is crucial for advancing precision breeding strategies. (2) Methods: This study investigated transcriptome differences in the longissimus dorsi muscle between Chinese Congjiang Xiang (CX) and Landrace [...] Read more.
(1) Objectives: Understanding the genetic basis of muscle development and meat quality traits in divergent pig breeds is crucial for advancing precision breeding strategies. (2) Methods: This study investigated transcriptome differences in the longissimus dorsi muscle between Chinese Congjiang Xiang (CX) and Landrace (LAN) pigs. RNA sequencing was performed on muscle tissues from ten individuals of each breed, generating 874.5 million raw reads with an average mapping rate of 89.3% to the pig reference genome. (3) Results: Transcriptional profiling revealed distinct expression patterns with 785 genes exclusively expressed in CX pigs and 457 genes unique to LAN pigs, while 7099 co-expressed genes were shared by both breeds. Differential expression analysis identified 2459 significantly different genes (|log2FC| ≥ 1, adjusted p-value < 0.05), with 1745 up-regulated and 714 down-regulated in CX pigs. Among the most significantly up-regulated genes in CX pigs were flavor-associated genes (ELOVL5/6, FASN, DGAT2, ALDH1A3, PPAR-γ) with log2FC values ranging from 1.21 to 3.88. GO and KEGG pathway analyses revealed that up-regulated genes in CX pigs were significantly enriched in immune response pathways (adjusted p-value < 0.01), while down-regulated genes were primarily associated with myosin complex formation and PPAR signaling pathway. PPI network analysis identified PPAR-γ as a central hub gene with 16 direct interactions to other flavor-related genes. (4) Conclusions: These findings demonstrate that the superior meat flavor characteristics of indigenous Chinese pigs are driven by enhanced expression of lipid metabolism genes and distinctive immune-related pathways, providing specific molecular targets for breeding programs aimed at improving meat quality while maintaining production efficiency in commercial breeds. Full article
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25 pages, 1223 KiB  
Review
The Impact of Cattle Grazing on Shrub Biomass: A Review on Temperate Ecosystems
by Dimitrios Oikonomou, Maria Yiakoulaki, Yannis Kazoglou, Michael Vrahnakis and Gavriil Xanthopoulos
Land 2025, 14(6), 1277; https://doi.org/10.3390/land14061277 - 14 Jun 2025
Viewed by 711
Abstract
Cattle grazing is particularly important to natural and semi-natural ecosystems, having often replaced grazing by smaller domestic ruminants such as goats and sheep. While cattle are mainly considered grazers rather than browsers, the pressures, direct or indirect, they exert on shrub encroachment are [...] Read more.
Cattle grazing is particularly important to natural and semi-natural ecosystems, having often replaced grazing by smaller domestic ruminants such as goats and sheep. While cattle are mainly considered grazers rather than browsers, the pressures, direct or indirect, they exert on shrub encroachment are significant. Thus, their grazing and browsing activities can often be considered complementary to ecosystem management, especially in landscapes characterized by shrub presence and frequent wildfires. Several factors may influence the impact of cattle browsing, including the stocking rate, the specific breed of cattle, and their adaptation to the respective ecosystem, as well as the particular type of ecosystem. This review examines the impact of cattle browsing on shrubs across various temperate ecosystems. Findings indicate that cattle usually consume only 5–10% of woody forage, but exceptional browsers like Highland cattle can consume up to 45%, making them promising for controlling shrub encroachment. Nevertheless, grazing often negatively impacts shrub richness, especially when combined with management interventions or wildfires, thereby raising concerns about plant regeneration. Future research should prioritize the ecological value of indigenous browsing cattle breeds over productivity-focused goals; however, several studies fail to specify the breeds examined, thereby limiting the ability to draw breed-specific conclusions. Full article
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