Animal genetics最新文献

In Friesian horses, withers height is an important trait as a minimum has been set to be eligible to the studbook. Several loci for withers height have been identified in horses. However, withers height has not been studied in the Friesian horse. Therefore, our aim was to identify loci associated with withers height in the Friesian horse population. We performed a genome-wide association study using 70 K SNP data of 2192 Friesian horses. We found ECA1 and ECA9 to be significantly associated with withers height, explaining 19.6% and 3.5% of the phenotypic variance, respectively. In other horse breeds, the LCORL/NCPAG locus on ECA3 showed the strongest association with withers height, but here we found that the best-associated SNP for that locus is nearly fixed in Friesian horses for the allele associated with small size. Moreover, we observed a clear decline followed by a marked increase in average withers height of the Friesian horse over time, probably owing to shifts in its primary use over the course of the years. Additionally, the frequency of the best-associated SNP on ECA1 has increased over time. Together, our study showed that ECA1 and ECA9 are associated with withers height in Friesian horses. Further studies should be performed to confirm candidate causal mutations.

Omani Jabal Akhdar goats are highly valued for their resilience, superior growth rate and twinning rate compared with other Omani goat breeds. Therefore, understanding their genetic diversity and population structure is essential for sustainable breeding efforts and conservation of the breed. This study aimed to assess the genetic diversity and population structure of Jabal Akhdar goats with single nucleotide polymorphisms generated with the Illumina 50K Goat Chip. Multidimensional scaling analysis and Admixture analysis revealed that Jabal Akhdar goats possess a distinct genetic ancestry representing a mixture of the Asian and African goat lineages which highlights the historic maritime trading and interactions of the Omanis with both continents. The multidimensional scaling analysis and the Reynolds unweighted distances both indicated that Jabal Akhdar goats share a close genetic relationship with West Asian breeds such as Iranian Bezoar, the Australian Cashmere, and Turkish breeds such as the Kil goats, all of which are adapted to cold climates and high elevations. Notably, the breed exhibited a moderate genomic inbreeding level (FPlink = 0.219 and FROH = 0.047), comparable with other West Asian breeds, indicating adequate levels of genetic diversity. This study represents the first genome-wide characterization of the Jabal Akhdar goat breed. Despite its moderate inbreeding levels, attention should be focused on conservation efforts to safeguard the distinctive genetic diversity of Jabal Akhdar goats to prevent the erosion of its genetic diversity or admixture with exotic commercial breeds.

Gene editing and genome manipulation offer great promise for treating diseases in both humans and animals. There is a danger, however, that this technology could be used for other purposes such as performance enhancement. To detect such ‘gene doping’ events, we evaluated a targeted enrichment panel and next-generation sequencing to assess its reproducibility, sensitivity, and capability of variant detection on a wide variety of samples and biological matrices. The panel was verified against existing data for the myostatin gene, a PCR-based SNP panel, and whole genome sequencing in a subset of samples. As successful detection of seamless edits will rely on a detailed understanding of the natural population, we also screened over 170 Thoroughbreds and catalogued numerous novel variants. These included several resulting in coding alterations, and a structural variant. Samples spiked with transgenic cDNA-based material to simulate gene doping events were detected down to 3.2% mosaicism, giving confidence that mosaic mutations resulting from embryonic introduction of gene editing reagents can be detected using these methods. The ability of software packages to detect gene doping events was also assessed, including multiple genome alignment tools, variant callers, and structural variant callers. Freebayes performed strongest at SNP-based editing detection, and Delly and Manta had complementary advantages depending on the mutation type. For routine testing, a multi-faceted approach to calling should be taken to maximise the detection capabilities.

Pork is an essential source of fatty acids (FAs) in the human diet. Fatty acids are important for various biological processes and can impact transcription regulation. The primary objective of this study was to identify candidate functional single nucleotide polymorphisms (SNPs) and expression quantitative trait loci (eQTL) associated with FA composition variation, and transcription factors (TFs) related to lipid metabolism using SNP array genotyping and Longissimus lumborum muscle transcriptome of Large White pigs. A total of 105 378 unique SNPs were identified, including 74 955 originating from RNA-Seq data and 30 423 SNPs from the Porcine 50K SNP chip. These SNPs were tested for association with the skeletal muscle gene expression data (15 090 genes) using the matrixeqtl package. Genome-wide association studies were conducted to test the association of these SNPs with FA trait variation, resulting in 74 254 eQTL, including 15 558 cis- and 58 696 trans-eQTL. Furthermore, 23 eQTL hotspots were identified, along with four TFs related to lipid metabolism: EGR1, SP1, CREB3 and INSM. The analysis identified two SNPs significantly associated with oleic and linolenic acids in the skeletal muscle of pigs. Candidate genes previously reported to influence meat quality in pigs and human health were identified, including PITX3, NT5C2, FTL, GLIS1, API5 and HILPDA. Although these findings offer valuable insights into metabolic disease response and lipid metabolism, contributing to a better understanding of gene expression related to lipid metabolism, meat quality and FA composition in pigs, the limited sample size indicates that further validations using larger datasets are recommended.

Llama breeding is an important source of economic income for Andean communities, thus ensuring llama biodiversity is fundamental to making breeding decisions that promote sustainable production. Despite this, there is limited information on the genetic diversity of llama populations in Argentina. Moreover, some llama herds in the northwest region of the country exhibit low reproductive efficiency and a high incidence of congenital abnormalities. In this study, we used genotyping by sequencing, a genome-wide approach, to estimate the genetic diversity of Argentine llama populations, assess their conservation status and inbreeding levels, and discuss the impacts on breeding. Overall, our results indicate that current llama populations in the northwest present moderate to high genetic diversity, although a recent reduction in population size was detected for two of them. Population structure was subtle, although three clusters, with some substructure, were recognized. The inbreeding coefficient values were similar for all populations showing moderate to high inbreeding levels. There was a predominance of short homozygous segments, which is indicative of ancient consanguinity. However, recent autozygosity events were evidenced in some llamas with congenital disorders. Thus, we investigated the chromosomal region to find potential candidate genes for such traits. The genes MYO15A and USH1G are proposed as candidates for pigmentation-associated deafness, although further research is needed. This study establishes an initial step towards understanding the genetic diversity of Argentine llamas, highlighting the necessity of reducing current inbreeding levels and implementing continuous monitoring to improve breeding decisions and support a sustainable production system for the species.

This study investigated the heat stress response in Holstein Friesian and Sahiwal cattle by examining DNA methylation markers in the HSP70 gene promoter. Heat stress parameters such as temperature–humidity index (THI), average rectal temperature (ART), and heat tolerance coefficient (HTC) were analyzed alongside mRNA production during summer and winter. Blood samples were collected from both Holstein Friesian and Sahiwal cattle breeds to assess heat stress parameters, including THI, ART, and HTC. Seasonal variations in these heat stress parameters were evaluated along with mRNA expression levels. The DNA methylation pattern in the HSP70 gene promoter was assessed using the AvaI enzyme while gene expression was analyzed via quantitative PCR with PPIA as a control. Significant correlations were found between seasons, breed-specific heat stress parameters, HSP70 expression, and DNA methylation. Both Sahiwal and Holstein Friesian cattle exhibited higher HTC when DNA methylation was absent, with Sahiwal cattle consistently demonstrating greater heat tolerance than Holstein Friesians. This study highlights the complex interplay between seasonal changes, breed-specific adaptations, and epigenetic modifications in cattle's heat stress responses. The upregulated HSP70 expression suggests a role in thermotolerance. However, the study focused on a single DNA methylation change; broader investigations into additional epigenetic modifications are needed to fully understand heat stress resilience mechanisms across cattle populations.

Ichthyoses are a heterogenous group of inherited disorders that are characterized by excessive scale formation on the skin. We investigated a Chihuahua with severe scaling since age 12 weeks. The scaling was generalized and involved the entire body and legs. The paw pads were mildly hyperkeratotic. The clinical features together with histopathological findings in skin biopsies were compatible with non-epidermolytic ichthyosis. To identify a potential genetic cause of the ichthyosis, we sequenced the genome of the affected dog and compared the data to 1567 control genomes. Filtering for private variants identified a homozygous missense variant in ALOXE3, XP_038392720.1:p.(Gly460Asp). ALOXE3 is a known candidate gene for ichthyosis in humans and encodes arachidonate epidermal lipoxygenase 3. The enzyme is involved in the production of a functional corneocyte lipid envelope, an essential component of the epidermal barrier. Pathogenic variants in ALOXE3 have been described in human patients with autosomal recessive congenital ichthyosis. We assume that the identified missense variant in the affected Chihuahua of this study impairs the normal function of the ALOXE3 protein and the formation of a functioning corneocyte lipid envelope, which ultimately leads to a disorder of cornification that manifests as ichthyosis. To the best of our knowledge, this is the first report of a spontaneous ALOXE3 variant in domestic animals.

Guppy (Poecilia reticulata) is a popular tropical ornamental fish with high phenotypic diversity. This study investigates the genetic basis of the red-eyed trait (ocular albinism) in guppy through hybridization between the sky-blue strain (red-eyed) and the red-fun strain (black-eyed). Our results demonstrated black eye to be the dominant trait relative to red eye, and that the ratio of the number of black-eyed guppies to that of red-eyed ones in the F2 generation is consistent with 3:1, which indicates that the red-eyed trait in the sky-blue strain guppies conforms to the model of Mendelian monogenic inheritance. To identify candidate genes associated with the red-eyed trait in guppies, we conducted a genome-wide association study using 65 F2 individuals (23 red-eyed and 42 black-eyed). A total of 106 genes showed significant associations with the red-eyed trait in guppy and OCA2 was considered as the most important candidate gene. This study provides a reference for insights into the molecular mechanisms underlying ocular albinism in guppy.

Mastitis is a major health and economic threat to the dairy industry, causing massive losses every year worldwide. Staphylococcus aureus is the chief pathogen, responsible for most of the subclinical as well as a considerable portion of the clinical cases. Conventional control strategies, including antibiotic treatment and genetic selection for resistance, have shown limited success due to antimicrobial resistance and low heritability of mastitis resilience traits. This calls for the exploration of novel approaches such as epigenetics, that offers insights into host–pathogen interactions beyond the genetic variations. This review focuses on DNA methylation changes in the mammary gland that occur during S. aureus mastitis. Recent research has identified immune suppression and pathogen persistence in relation with DNA methylation during the disease. The microbe has been reported to alter the methylation status of regulatory regions for many immune genes such as CXCR1, TNF-α, IL6R, IL10, and C3, resulting in dysregulation of immune responses in the host, thereby facilitating pathogen persistence and chronic infection. Along with its own virulence factors, differential DNA methylation status of such genes during infection helps the pathogen to escape host defence, and decreases the intensity of inflammation. Thus, understanding these mechanisms can open new avenues in the field of disease diagnosis, animal selection, and immunotherapy among others. Such an integrative approach offers a revolution in mastitis control strategies, ensuring better health and productivity in dairy animals. © 2025 Stichting International Foundation for Animal Genetics.