Animal genetics最新文献

{"title":"Genotype-by-environment interactions in beef and dairy cattle populations: A review of methodologies and perspectives on research and applications","authors":"João B. Silva Neto,&nbsp;Lucio F. M. Mota,&nbsp;Marisol Londoño-Gil,&nbsp;Patrícia I. Schmidt,&nbsp;Gustavo R. D. Rodrigues,&nbsp;Viviane A. Ligori,&nbsp;Leonardo M. Arikawa,&nbsp;Claudio U. Magnabosco,&nbsp;Luiz F. Brito,&nbsp;Fernando Baldi","doi":"10.1111/age.13483","DOIUrl":"10.1111/age.13483","url":null,"abstract":"<p>Modern livestock production systems are characterized by a greater focus on intensification, involving managing larger numbers of animals to achieve higher productive efficiency and animal health and welfare within herds. Therefore, animal breeding programs need to be strategically designed to select animals that can effectively enhance production performance and animal welfare across a range of environmental conditions. Thus, this review summarizes the main methodologies used for assessing the levels of genotype-by-environment interaction (G × E) in cattle populations. In addition, we explored the importance of integrating genomic and phenotypic information to quantify and account for G × E in breeding programs. An overview of the structure of cattle breeding programs is provided to give insights into the potential outcomes and challenges faced when considering G × E to optimize genetic gains in breeding programs. The role of nutrigenomics and its impact on gene expression related to metabolism in cattle are also discussed, along with an examination of current research findings and their potential implications for future research and practical applications. Out of the 116 studies examined, 60 and 56 focused on beef and dairy cattle, respectively. A total of 83.62% of these studies reported genetic correlations across environmental gradients below 0.80, indicating the presence of G × E. For beef cattle, 69.33%, 24%, 2.67%, 2.67%, and 1.33% of the studies evaluated growth, reproduction, carcass and meat quality, survival, and feed efficiency traits, respectively. By contrast, G × E research in dairy cattle populations predominantly focused on milk yield and milk composition (79.36% of the studies), followed by reproduction and fertility (19.05%), and survival (1.59%) traits. The importance of G × E becomes particularly evident when considering complex traits such as heat tolerance, disease resistance, reproductive performance, and feed efficiency, as highlighted in this review. Genomic models provide a valuable avenue for studying these traits in greater depth, allowing for the identification of candidate genes and metabolic pathways associated with animal fitness, adaptation, and environmental efficiency. Nutrigenetics and nutrigenomics are emerging fields that require extensive investigation to maximize our understanding of gene–nutrient interactions. By studying various transcription factors, we can potentially improve animal metabolism, improving performance, health, and quality of products such as meat and milk.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/age.13483","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142387399","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":"Genome-wide re-sequencing reveals regulatory genes and variants involved in the regulation of intermittent fertilization intensity in Wenchang chickens","authors":"Xiuping Wang,&nbsp;Lei Wang,&nbsp;Xing Hong,&nbsp;Mingze Li,&nbsp;Xianyuan Gu,&nbsp;Minhui Liu,&nbsp;ShiJun Li","doi":"10.1111/age.13471","DOIUrl":"10.1111/age.13471","url":null,"abstract":"<p>Intermittent fertilization intensity (IFI) is closely related to higher fertilization in chickens, but the genetic basis of IFI is not clearly understood. Here, we sampled a total of 939 Wenchang chickens with IFI. The IFI traits had negative correlation with the fertilization rate and exhibited huge phenotypic variations among individuals of the same strain. Based on SNPs derived from a subset of 499 whole genome data, a genome-wide association study with mixed linear model and further linkage disequilibrium analysis were performed to test potential associations between IFI traits and genomic variants. We identified 35 SNP variants and a 19.82 kb linkage disequilibrium block on chr8 significantly associated with IFI. This block is in the intron of LOC101750715, which shows significant homology with the human LMO4. Therefore, LOC101750715 and LMO4 may regulate IFI. The oviduct's immune regulation is crucial for fertilization. LMO4, activated by IL-6 and IL-23, promotes inflammation in epithelial cells. Thus, LOC101750715 and LMO4 may affect fertilization by regulating oviductal inflammation, impacting IFI. Our findings will provide targets for molecular-marker selection and genetic manipulation for lines of chickens with lower IFI.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142339547","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":"Identification of a functional single nucleotide polymorphism in the FASN promoter associated with milk fat traits in dairy cattle","authors":"Mélissa Poncet,&nbsp;Maureen Féménia,&nbsp;Mathieu Charles,&nbsp;Maxime Ben Braiek,&nbsp;Lorraine Bourgeois-Brunel,&nbsp;Hiroaki Taniguchi,&nbsp;Nathalie Duprat,&nbsp;Arnaud Boulling,&nbsp;Véronique Blanquet,&nbsp;Dominique Rocha","doi":"10.1111/age.13477","DOIUrl":"10.1111/age.13477","url":null,"abstract":"&lt;p&gt;In the past decades, multiple genome-wide association studies have been performed to identify loci affecting milk production traits, including some using imputed whole-genome sequence data (i.e. Daetwyler et al., &lt;span&gt;2014&lt;/span&gt;; Fang &amp; Pausch, &lt;span&gt;2019&lt;/span&gt;; Sanchez et al., &lt;span&gt;2017&lt;/span&gt;). Several genome-wide association studies have linked a polymorphism (rs136067046, BTA19: g.50775172 C&gt;G on ARS-UCD1.2) located in the upstream region of &lt;i&gt;FASN&lt;/i&gt; (encoding fatty acid synthase) to milk fat traits in dairy cattle (Cai et al., &lt;span&gt;2020&lt;/span&gt;; Sanchez et al., &lt;span&gt;2019&lt;/span&gt;; Tribout et al., &lt;span&gt;2020&lt;/span&gt;). For example, Cai and collaborators showed that rs136067046 is associated to milk fat traits in Nordic Holstein cows. FASN is an enzyme that plays a critical role in de novo fatty acid synthesis in milk. Interestingly, rs136067046 is located within an ATAC peak (chr.19: 50 773 523–50 795 886) found in the mammary gland (Yuan et al., &lt;span&gt;2023&lt;/span&gt;). It is thus possible that rs136067046 is a functional variant that directly impacts these traits.&lt;/p&gt;&lt;p&gt;The ability of this SNP to alter transcription factor binding sites was then predicted with a custom script, as previously described (Ramírez-Ayala et al., &lt;span&gt;2021&lt;/span&gt;). This analysis suggests that rs136067046 modifies the binding sites of nine transcription factors (Table 1). Five of those transcription factors are expressed (transcript per million reads ≥0.5) in mammary gland tissue (Fang et al., &lt;span&gt;2020&lt;/span&gt;). Interestingly, three of those five transcription factors are from the Krüppel-like factor (KLF) family, a conserved class of transcription factors. It has been shown that KLF4 promotes milk fat synthesis in bovine mammary epithelial cells by targeting the &lt;i&gt;FASN&lt;/i&gt; promoter region (Wu et al., &lt;span&gt;2024&lt;/span&gt;). The authors have shown, using yeast one-hybrid assay, that KLF4 interacts directly with a part of the &lt;i&gt;FASN&lt;/i&gt; promoter region, encompassing the location of rs136067046. It has also been shown that KLF5 controls the expression of &lt;i&gt;FASN&lt;/i&gt; through an interaction with SREBBP-1 (Lee et al., &lt;span&gt;2009&lt;/span&gt;). In addition, inactivation of &lt;i&gt;KLF6&lt;/i&gt; in bovine mammary epithelial cells increases &lt;i&gt;FASN&lt;/i&gt; expression (Iqbal et al., &lt;span&gt;2022&lt;/span&gt;). These studies point to the important role played by these KLF transcription factors in the regulation of &lt;i&gt;FASN&lt;/i&gt;. All these findings suggest that, consequently, rs136067046 is potentially a regulatory variant that might alter the expression of &lt;i&gt;FASN&lt;/i&gt;.&lt;/p&gt;&lt;p&gt;To investigate the potential regulatory function of the rs136067046 variant, we constructed and then functionally tested two allele-specific recombinant promoter vectors using the dual-luciferase reporter system and the bovine mammary epithelial MAC-T cell line (Huynh et al., &lt;span&gt;1991&lt;/span&gt;). Details on the plasmid constructions and luciferase assays are provided in Supplementary Material S1. The construct with the G alle","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/age.13477","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142339548","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":"The role of G protein-coupled receptors and their ligands in animal domestication","authors":"Gunnar Kleinau,&nbsp;Bice Chini,&nbsp;Leif Andersson,&nbsp;Patrick Scheerer","doi":"10.1111/age.13476","DOIUrl":"10.1111/age.13476","url":null,"abstract":"<p>The domestication of plants and animals has resulted in one of the most significant cultural and socio-economical transitions in human history. Domestication of animals, including human-supervised reproduction, largely uncoupled particular animal species from their natural, evolutionary history driven by environmental and ecological factors. The primary motivations for domesticating animals were, and still are, producing food and materials (e.g. meat, eggs, honey or milk products, wool, leather products, jewelry and medication products) to support plowing in agriculture or in transportation (e.g. horse, cattle, camel and llama) and to facilitate human activities (for hunting, rescuing, therapeutic aid, guarding behavior and protecting or just as a companion). In recent years, decoded genetic information from more than 40 domesticated animal species have become available; these studies have identified genes and mutations associated with specific physiological and behavioral traits contributing to the complex genetic background of animal domestication. These breeding-altered genomes provide insights into the regulation of different physiological areas, including information on links between e.g. endocrinology and behavior, with important pathophysiological implications (e.g. for obesity and cancer), extending the interest in domestication well beyond the field. Several genes that have undergone selection during domestication and breeding encode specific G protein-coupled receptors, a class of membrane-spanning receptors involved in the regulation of a number of overarching functions such as reproduction, development, body homeostasis, metabolism, stress responses, cognition, learning and memory. Here we summarize the available literature on variations in G protein-coupled receptors and their ligands and how these have contributed to animal domestication.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/age.13476","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142339549","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":"Intragenic dystrophin (DMD) duplication variant in Entlebucher Mountain Dogs with Duchenne muscular dystrophy","authors":"Cleo Schwarz,&nbsp;Vidhya Jagannathan,&nbsp;Claude Schelling,&nbsp;Tosso Leeb","doi":"10.1111/age.13475","DOIUrl":"10.1111/age.13475","url":null,"abstract":"<p>Muscular dystrophies represent a group of disorders characterized by progressive muscle degeneration and weakness. An important subgroup are the dystrophin-related muscular dystrophies caused by variants in the <i>DMD</i> gene. They can be divided into the more severe Duchenne muscular dystrophy and the milder Becker muscular dystrophy. Here, we characterize the clinical, histopathological and molecular genetic aspects of two male Entlebucher Mountain Dogs with clinical signs of muscular dystrophy. The two dogs presented with marked dysphagia starting at the age of several weeks and in the later course recognizable exercise intolerance with highly increased serum creatine kinase levels. Histopathological signs of a dystrophic myopathy represented by degeneration of muscle fibers and signs of regeneration were present. Whole genome sequencing of one affected dog identified an intragenic 8.6 kb duplication in the X-chromosomal <i>DMD</i> gene, c.7528-4048_7645 + 4450dup. No other protein-changing variants in candidate genes for muscular dystrophy were identified. The duplication includes exon 52 of <i>DMD</i> and is predicted to lead to a frameshift and truncation of 30% of the wild-type open reading frame. Genotyping of the whole family confirmed the presence of the mutant allele in both affected dogs and the unaffected dam. The correct co-segregation of the mutant allele in the affected family as well as knowledge from humans and other species suggest the identified <i>DMD</i> variant as the most likely candidate variant for the muscular dystrophy phenotype in the two investigated dogs.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/age.13475","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142279393","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":"The African introgression of Murciano Granadina goats has a Moroccan origin and displays remarkable levels of inter-individual variability","authors":"E. Petretto,&nbsp;M. G. Luigi-Sierra,&nbsp;G. M. Vacca,&nbsp;A. Martínez,&nbsp;J. V. Delgado,&nbsp;J. Fernández Álvarez,&nbsp;A. Castelló,&nbsp;M. Pazzola,&nbsp;J. Jordana,&nbsp;M. L. Dettori,&nbsp;M. Amills","doi":"10.1111/age.13472","DOIUrl":"10.1111/age.13472","url":null,"abstract":"<p>There is evidence that Murciano Granadina (MG), the most important caprine dairy breed in Spain, has been introgressed by African goats, but the precise geographic origin of such introgression has not been identified yet. Moreover, an accurate estimate of the magnitude of this African introgression is lacking, since current estimates are based on small numbers of sampled individuals. The aim of our work was to tackle these two issues by genotyping 500 MG goats with the Goat SNP50 BeadChip and comparing their genotypes with those of reference populations from Spain (<i>Bermeya</i>), France (<i>Saanen</i>), Morocco (<i>Barcha</i>, <i>Draa</i>, <i>Ghazalia</i>, <i>Noire de Atlas</i>, <i>Nord</i>, <i>Moroccan</i>), Egypt (<i>Barki</i>, <i>Oasis</i>, <i>Saidi</i>), Algeria (<i>Arabia</i>, <i>Makatia</i>, <i>M'Zabite, Kabyle</i>), Tunisia (<i>Tunisian native breeds</i>) and Sudan (<i>Desert</i>, <i>Nilotic</i>, <i>Taggar</i>). The population of 500 MG goats was subdivided into 10 datasets of 50 individuals to ensure that sample sizes of the target (MG) and reference populations are balanced. Performance of an unsupervised ADMIXTURE analysis demonstrated that MG goats have a North African ancestry, with an average proportion of 4.4 ± 2.3%. Next, we did a supervised ADMIXTURE analysis that revealed that the Moroccan genetic component reaches a proportion of 4.01 ± 3.9% in MG goats, while the Algerian (0.001 ± 0.001%), Egyptian (0.2 ± 0.1%), Sudanese (0.1 ± 0.1%) and Tunisian (0.3 ± 0.4%) components are present in extremely small proportions. The historical circumstances of this introgression event are currently unknown, but several plausible scenarios are outlined. Moreover, our results show considerable inter-individual heterogeneity regarding the magnitude of the Moroccan introgression of MG goats (0%– 12% depending on the MG data set under analysis). This result implies that reliable estimates about the introgression of autochthonous livestock by exotic breeds can only be obtained by extensively sampling target populations.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/age.13472","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142261776","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":"ZFAT (isoform-specific) and its antisense RNA 1 (ZFAT-AS1) are two allele-specific monoallelically expressed genes in cattle","authors":"Yinjiao Zhang,&nbsp;Yunchang Zheng,&nbsp;Wenli Yu,&nbsp;Lidan Yang,&nbsp;Cui Zhang,&nbsp;Shujing Li,&nbsp;Shijie Li","doi":"10.1111/age.13473","DOIUrl":"10.1111/age.13473","url":null,"abstract":"<p>In mammals, imprinted genes are characterised by a monoallelic expression, which is based on parental origin and is essential for both foetal and placental development. The <i>ZFAT</i> gene encodes a transcriptional factor, and its non-coding antisense RNA, <i>ZFAT-AS1</i>, overlaps with the <i>ZFAT</i> locus. Both <i>ZFAT</i> and <i>ZFAT-AS1</i> are maternally imprinted in human placentas. In bovines, the imprinting status of the <i>ZFAT</i> and <i>ZFAT-AS1</i> genes has yet to be reported. In this study, we analysed the allelic expression of three transcript variants (X1–X3) of the bovine <i>ZFAT</i> and <i>ZFAT-AS1</i> genes in somatic tissues and placentas using a single nucleotide polymorphism-based method. The results showed that bovine <i>ZFAT</i> exhibited isoform-specific paternal expression. The <i>ZFAT</i> X2 variant exhibited monoallelic expression in the bovine placentas and biallelic expression in the six bovine somatic tissues (heart, liver, spleen, lung, kidney and brain). However, the <i>ZFAT</i> X1 and X3 variants were biallelically expressed in both bovine tissues and placentas. A 311 bp bovine <i>ZFAT-AS1</i> complementary DNA (cDNA) sequence was obtained by aligning the human <i>ZFAT-AS1</i> cDNA sequence with the bovine genome and conducting reverse transcription polymerase chain reaction amplification. Bovine <i>ZFAT-AS1</i> have monoallelic expression in bovine placentas and somatic tissues. In addition, the DNA methylation of two regions was characterised, including the partial promoter, and exon 1 and intron 1 regions of <i>ZFAT</i>, and there were no differentially methylated regions.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142131666","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":"Genomic responses to climatic challenges in beef cattle: A review","authors":"Daniele Colombi,&nbsp;Francesco Perini,&nbsp;Stefano Bettini,&nbsp;Salvatore Mastrangelo,&nbsp;Fabio Abeni,&nbsp;Giuseppe Conte,&nbsp;Donata Marletta,&nbsp;Martino Cassandro,&nbsp;Umberto Bernabucci,&nbsp;Roberta Ciampolini,&nbsp;Emiliano Lasagna","doi":"10.1111/age.13474","DOIUrl":"10.1111/age.13474","url":null,"abstract":"<p>Climate change is a major concern for the near future and for livestock breeding. Cattle breeding, due to its greenhouse gas emissions, is one of the most implicated industries. Consequently, the main future goals are to breed animals resilient to climate change, with the aim of lowering the livestock impact on the environment and selecting animals that will be able to resist different, unsuitable, and changing climates. The aim of this literature review is to compare the most recent studies on the response and adaptation of beef cattle breeds to extreme environments, in terms of genes and pathways involved. Beef breeding is just starting to implement genomics in its selection plans, and shedding light on the genomic responses to extreme climates could speed up and simplify the adaptation of these breeds to climate change. This review discusses the genes involved in climatic stress responses, including those related to extremely cold climates, in beef and dual-purpose cattle breeds. Genes were associated with productive traits, coat and skin structure and development, thermotolerance, cellular physiology and DNA repair mechanisms, immune system, and fertility traits. The knowledge of genes and pathways involved in climate resilience should be taken into consideration for further selection in beef cattle breeding and could promote the valorization of local breeds adapted to extreme environmental conditions. The use of local or resilient breeds could enhance the environmental and social sustainability, animal welfare, and production, compared with the introduction of cosmopolitan breeds with uncertain adaptation in uncontrolled environmental areas.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/age.13474","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142103694","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":"Core competing endogenous RNA network based on mRNA and non-coding RNA expression profiles in chicken fatty liver","authors":"Qingxing Xiao,&nbsp;Yonghong Zhang,&nbsp;Hongyu Ni,&nbsp;Yijing Yin,&nbsp;Anchong Gao,&nbsp;Benhai Cui,&nbsp;Wei Zhang,&nbsp;Yumei Li,&nbsp;Yuwei Yang","doi":"10.1111/age.13469","DOIUrl":"10.1111/age.13469","url":null,"abstract":"<p>Fatty liver disease is a common metabolic disease in chickens. This disease can lead to a decrease in egg production and increase the risk of death in chickens. Long non-coding RNAs (lncRNAs) are involved in fatty liver formation by directly targeting genes or regulating gene expression by competitively binding microRNAs. However, a large proportion of competing endogenous RNA (ceRNA) networks in fatty liver diseases are still unclear. The total of 300 Jingxing-Huang chickens were used for fatty liver model construction. Then, differentially expressed (DE) genes (DEGs) identified through whole-transcriptome sequencing from four chickens with fatty liver and four chickens without fatty liver were chosen from the F1 generation. A total of 953 DEGs were identified between the fatty liver group and the control group, including 26 DE micro (mi)RNAs and 56 DE lncRNAs. Differential expression heatmaps and volcano plots were obtained after clustering expression analysis. Gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses revealed that these DEGs were involved in many biological processes and signaling pathways related to fatty acid metabolism and lipid synthesis. Furthermore, <span>cytoscape</span> was used to construct a ceRNA network of the DE miRNAs, DE mRNAs, and DE lncRNAs. Eleven DE lncRNAs, seven DE miRNAs, and 13 DE mRNAs were found to be associated with the pathogenesis of fatty liver disease. An lncRNA–miRNA–mRNA ceRNA network was constructed to elucidate the mechanisms of fatty liver diseases, and the ENSGALT00000079786-miR-140/miR-143/miR-1a/miR-22/miR-375 network was identified. These results provide a valuable resource for further elucidating the posttranscriptional regulatory mechanisms of chicken liver and adipose fat development or deposition.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142008148","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":"Exonisation of an intronic L1 element in the dystrophin gene associated with X-linked muscular dystrophy in a Border Collie dog","authors":"Mario Van Poucke,&nbsp;Liesbet Ledeganck,&nbsp;Ling T. Guo,&nbsp;G. Diane Shelton,&nbsp;Sofie F. M. Bhatti,&nbsp;Ine Cornelis,&nbsp;Luc Peelman","doi":"10.1111/age.13470","DOIUrl":"10.1111/age.13470","url":null,"abstract":"<p>X-linked recessive dystrophinopathies are the most common muscular dystrophies (MDs) in humans and dogs. To date, 20 breed-specific MD-associated variants are described in the canine <i>dystrophin</i> gene (<i>DMD</i>), including one associated with dystrophin-deficient MD in the Border Collie mixed breed. Here, we report the diagnosis and follow-up of mild dystrophin-deficient MD in a 5-month-old male Border Collie, associated with a novel <i>DMD</i> variant. Diagnosis was based on neurological examination and laboratory evaluations including creatine kinase activity, electromyography and muscle biopsies with immunofluorescent staining. Inspection of the Sashimi plots of the RNA-seq data from the affected muscle biopsy led to the discovery of a 162-bp L1 pseudoexon in <i>DMD</i> intron 63, introducing a frameshift and a premature stop codon (NM_001003343.1: c.9271_9272insN[162] p.(Ala3091fs*21)). Reduced <i>DMD</i> mRNA levels were detected for both the non-pseudoexon (50× less) and pseudoexon (3× less) containing transcripts in the affected muscle, compared with the level of the non-pseudoexon containing transcript in a control muscle, resulting in very low dystrophin protein levels and the upregulation of utrophin. Because the variant was only found in the affected dog, not in the healthy mother and grandmother, or in 108 unrelated Border Collies from the Belgian population (46 males and 62 females), it was considered a <i>de novo</i> variant. Although the prognosis for dystrophinopathy is generally regarded as poor, the dog stabilised at the age of 6 months and is still clinically stable at the age of 2 years.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-08-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141995058","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}