Animal genetics最新文献

{"title":"Transcription factors and candidate functional SNPs associated with variation in fatty acid composition from skeletal muscle of pigs","authors":"Mariah C. Durval,&nbsp;Luiz F. Brito,&nbsp;Simara L. Fanalli,&nbsp;Artur O. Rocha,&nbsp;Lorena F. Benfica,&nbsp;Fernanda N. Ciconello,&nbsp;Camila S. Oliveira,&nbsp;Ingrid S. Garcia,&nbsp;Felipe A. Oliveira Freitas,&nbsp;Lucas E. Nascimento,&nbsp;Bruna P. Martins da Silva,&nbsp;Bárbara Silva-Vignato,&nbsp;Aline S. M. Cesar","doi":"10.1111/age.70051","DOIUrl":"https://doi.org/10.1111/age.70051","url":null,"abstract":"<p>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 <span>matrixeqtl</span> 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 <i>cis</i>- and 58 696 <i>trans-</i>eQTL. Furthermore, 23 eQTL hotspots were identified, along with four TFs related to lipid metabolism: <i>EGR1</i>, <i>SP1</i>, <i>CREB3</i> and <i>INSM</i>. 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 <i>PITX3</i>, <i>NT5C2</i>, <i>FTL</i>, <i>GLIS1</i>, <i>API5</i> and <i>HILPDA</i>. 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.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"56 5","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/age.70051","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145272493","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genotyping by sequencing-based genetic insights into Argentine llama populations and breeding impacts","authors":"M. Anello,&nbsp;M. Muzzio,&nbsp;M. B. Silbestro,&nbsp;M. S. Daverio,&nbsp;R. Unzaga,&nbsp;S. R. Romero,&nbsp;F. Rigalt,&nbsp;L. Vidal Rioja,&nbsp;F. Di Rocco","doi":"10.1111/age.70053","DOIUrl":"10.1111/age.70053","url":null,"abstract":"<p>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 <i>MYO15A</i> and <i>USH1G</i> 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.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"56 5","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145249469","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative analysis of heat stress response in Holstein Friesian and Sahiwal cattle through HSP70 gene expression and promoter DNA methylation","authors":"Fariha,&nbsp;Muhammad Shakeel Shabbir,&nbsp;Saima Anwar,&nbsp;Hamda Azmat,&nbsp;Muhammad Bilal Bin Majeed,&nbsp;Haiba Kaul","doi":"10.1111/age.70048","DOIUrl":"10.1111/age.70048","url":null,"abstract":"<p>This study investigated the heat stress response in Holstein Friesian and Sahiwal cattle by examining DNA methylation markers in the <i>HSP70</i> 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 <i>HSP70</i> 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.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"56 5","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145249411","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"ALOXE3 missense variant in a Chihuahua with autosomal recessive ichthyosis","authors":"Carina Vinberg,&nbsp;Stefan J. Rietmann,&nbsp;Sara Soto,&nbsp;Vidhya Jagannathan,&nbsp;Susanne Åhman,&nbsp;Tosso Leeb","doi":"10.1111/age.70055","DOIUrl":"10.1111/age.70055","url":null,"abstract":"<p>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 <i>ALOXE3</i>, XP_038392720.1:p.(Gly460Asp). <i>ALOXE3</i> 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 <i>ALOXE3</i> 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 <i>ALOXE3</i> variant in domestic animals.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"56 5","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12503983/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145243563","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A genome-wide association study for the red-eyed trait (ocular albinism) in an F2 population of guppy (Poecilia reticulata)","authors":"Ying Chang,&nbsp;Shenjun Wu,&nbsp;Junying Li,&nbsp;Haigang Bao,&nbsp;Changxin Wu","doi":"10.1111/age.70045","DOIUrl":"10.1111/age.70045","url":null,"abstract":"<p>Guppy (<i>Poecilia reticulata</i>) 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 <i>OCA2</i> was considered as the most important candidate gene. This study provides a reference for insights into the molecular mechanisms underlying ocular albinism in guppy.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"56 5","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145243640","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A new Editor-in-Chief","authors":"Johannes A. Lenstra","doi":"10.1111/age.70046","DOIUrl":"10.1111/age.70046","url":null,"abstract":"","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"56 5","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145205352","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Decoding DNA methylation in Staphylococcus aureus mastitis: Implications for immune regulation and disease resistance","authors":"Apeksha,&nbsp;Abhishek Mahendra Todkari,&nbsp;Ashok Chaudhary,&nbsp;Mir Mehroz Hassan,&nbsp;Diksha Upreti,&nbsp;Shri Ram Saini,&nbsp;Sheikh Firdous Ahmad,&nbsp;Ashwni Kumar Pandey","doi":"10.1111/age.70044","DOIUrl":"https://doi.org/10.1111/age.70044","url":null,"abstract":"<p>Mastitis is a major health and economic threat to the dairy industry, causing massive losses every year worldwide. <i>Staphylococcus aureus</i> 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 <i>S. aureus</i> 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 <i>CXCR1</i>, <i>TNF-α</i>, <i>IL6R</i>, <i>IL10</i>, and <i>C3</i>, 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.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"56 5","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/age.70044","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145146546","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic factors for hematological traits in pigs","authors":"Jiahong Sun,&nbsp;Emil Ibragimov,&nbsp;Peter Karlskov-Mortensen,&nbsp;Merete Fredholm","doi":"10.1111/age.70043","DOIUrl":"10.1111/age.70043","url":null,"abstract":"<p>Complete blood count with differential is a critical diagnostic tool for evaluating the physiological and health status of individuals by analyzing white blood cells, red blood cells, and platelets. While extensively used in human medicine, the application of complete blood count biomarkers in pigs remain limited. This review focuses on the genetic architecture of hematological traits in pigs (Sus scrofa) using data from genetic association studies. By compiling data from multiple porcine studies, we identified 509 SNPs within 53 high-confidence QTL supported by more than one study. Among these, 37 QTL were homologous to human loci, with 19 containing plausible candidate genes likely to be influencing hematological traits. These genes are often linked to cytoskeletal formation, hematopoiesis, and immune function, highlighting conserved biological mechanisms across species. Our findings provide a foundation for further investigations into the genetic regulation of blood cell parameters in pigs and their implications for health, welfare, and production traits, offering potential translational insights for both veterinary and human medicine.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"56 5","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/age.70043","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145084608","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"IMAGE001: A new livestock multispecies SNP array to characterize genomic variation in European livestock gene bank collections","authors":"R. P. M. A. Crooijmans,&nbsp;R. Gonzalez Prendes,&nbsp;L. Colli,&nbsp;M. Del Corvo,&nbsp;M. Barbato,&nbsp;E. Somenzi,&nbsp;G. Tosser-Klopp,&nbsp;G. Meszaros,&nbsp;P. Ajmone-Marsan,&nbsp;S. Weigend,&nbsp;B. Wallner,&nbsp;M. E. McCue,&nbsp;L. Orlando,&nbsp;D. Bradley,&nbsp;S. J. Hiemstra,&nbsp;D. Schokker,&nbsp;N. Peynot,&nbsp;A. Stella,&nbsp;G. Restoux,&nbsp;M. A. M. Groenen,&nbsp;M. Tixier-Boichard","doi":"10.1111/age.70039","DOIUrl":"10.1111/age.70039","url":null,"abstract":"<p>Molecular genetic characterization of genetic resources is essential to study biodiversity. Whereas whole genome sequencing is still relatively expensive, low density SNP arrays offer a cost-effective and standardized solution. However, most of the current arrays are species specific. Their high SNP density often exceeds diversity mapping requirements and remains too costly for many genetic resource managers. The IMAGE H2020 project aimed at developing a low-cost multispecies SNP array to facilitate mapping of the genetic diversity in samples stored in gene banks and in vivo (on farm) traditional populations. This farm animal multispecies array contains approximately 10 K SNPs per species. The species included are cattle, sheep, goat, horse, pig, and chicken. We developed and tested this array on many samples from each of the six species. We describe here the SNP coverage and informativity across 253 breeds. We show that the array can be used to cluster local breeds according to history and genetic diversity. We illustrate its use for parentage testing. The array is publicly available at a reasonable price if ordered in multiples of 384 samples, leading to an overall cost of genotyping of approximately 15 euros per sample.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"56 5","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12445162/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145079483","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic variations for bean color of duck beak revealed by genome-wide association study","authors":"Jingjing Qi,&nbsp;Qian Hu,&nbsp;Yang Xi,&nbsp;Zhao Yang,&nbsp;Mengru Xu,&nbsp;Liang Li,&nbsp;Lili Bai,&nbsp;Hehe Liu","doi":"10.1111/age.70040","DOIUrl":"10.1111/age.70040","url":null,"abstract":"<p>The beak bean, found only in waterfowl and Galliformes, aids in foraging, self-defense and pecking hard objects. Its rich coloration results from prolonged evolutionary adaptation. This study analyzed beak bean phenotypes of duck at 10, 20, 30 and 40 days of age, revealing that the most common type is the black beak bean, characterized by melanin deposition on the beak surface. This study performed single nucleotide polymorphism (SNP)-based genome-wide association studies (GWASs) to investigate the genetic basis of beak bean color, identifying signals on chromosome 1. The copy number variation region-based GWAS revealed a consistent candidate region overlapping with the SNP-based GWAS signals, further supporting the importance of this genomic region. Locus zoom analysis further refined the candidate regions to 48.5–50.5 and 50.8–52.8 Mb. Functional enrichment analysis highlighted six candidate genes within these regions: <i>KITLG</i>, <i>DUSP6</i>, <i>GALNT4</i>, <i>MGAT4C</i>, <i>ATP2B1</i> and <i>NTS</i>. Notably, <i>KITLG</i> and <i>DUSP6</i>, which are linked to melanin production, were identified as key candidate genes for beak bean color. Our finding revealed the genetic basis of the bean color traits for the first time in ducks, providing a theoretical foundation and technological framework for enhancing duck beak coloration.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"56 5","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145079546","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}