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Intragenic dystrophin (DMD) duplication variant in Entlebucher Mountain Dogs with Duchenne muscular dystrophy. 患有杜氏肌营养不良症的 Entlebucher 山地犬基因内肌营养不良蛋白 (DMD) 复制变异。
IF 1.8 3区 生物学
Animal genetics Pub Date : 2024-09-22 DOI: 10.1111/age.13475
Cleo Schwarz, Vidhya Jagannathan, Claude Schelling, Tosso Leeb
{"title":"Intragenic dystrophin (DMD) duplication variant in Entlebucher Mountain Dogs with Duchenne muscular dystrophy.","authors":"Cleo Schwarz, Vidhya Jagannathan, Claude Schelling, Tosso Leeb","doi":"10.1111/age.13475","DOIUrl":"https://doi.org/10.1111/age.13475","url":null,"abstract":"<p><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 DMD 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 DMD 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 DMD 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 DMD 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":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The African introgression of Murciano Granadina goats has a Moroccan origin and displays remarkable levels of inter-individual variability Murciano Granadina 山羊的非洲引种源于摩洛哥,个体间变异程度显著
IF 2.4 3区 生物学
Animal genetics Pub Date : 2024-09-18 DOI: 10.1111/age.13472
E. Petretto, M. G. Luigi-Sierra, G. M. Vacca, A. Martínez, J. V. Delgado, J. Fernández Álvarez, A. Castelló, M. Pazzola, J. Jordana, M. L. Dettori, M. Amills
{"title":"The African introgression of Murciano Granadina goats has a Moroccan origin and displays remarkable levels of inter-individual variability","authors":"E. Petretto, M. G. Luigi-Sierra, G. M. Vacca, A. Martínez, J. V. Delgado, J. Fernández Álvarez, A. Castelló, M. Pazzola, J. Jordana, M. L. Dettori, M. Amills","doi":"10.1111/age.13472","DOIUrl":"https://doi.org/10.1111/age.13472","url":null,"abstract":"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.","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
ZFAT (isoform-specific) and its antisense RNA 1 (ZFAT-AS1) are two allele-specific monoallelically expressed genes in cattle. ZFAT(同工酶特异性)及其反义 RNA 1(ZFAT-AS1)是牛体内两个等位基因特异性的单平行表达基因。
IF 1.8 3区 生物学
Animal genetics Pub Date : 2024-09-04 DOI: 10.1111/age.13473
Yinjiao Zhang, Yunchang Zheng, Wenli Yu, Lidan Yang, Cui Zhang, Shujing Li, Shijie Li
{"title":"ZFAT (isoform-specific) and its antisense RNA 1 (ZFAT-AS1) are two allele-specific monoallelically expressed genes in cattle.","authors":"Yinjiao Zhang, Yunchang Zheng, Wenli Yu, Lidan Yang, Cui Zhang, Shujing Li, Shijie Li","doi":"10.1111/age.13473","DOIUrl":"https://doi.org/10.1111/age.13473","url":null,"abstract":"<p><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 ZFAT gene encodes a transcriptional factor, and its non-coding antisense RNA, ZFAT-AS1, overlaps with the ZFAT locus. Both ZFAT and ZFAT-AS1 are maternally imprinted in human placentas. In bovines, the imprinting status of the ZFAT and ZFAT-AS1 genes has yet to be reported. In this study, we analysed the allelic expression of three transcript variants (X1-X3) of the bovine ZFAT and ZFAT-AS1 genes in somatic tissues and placentas using a single nucleotide polymorphism-based method. The results showed that bovine ZFAT exhibited isoform-specific paternal expression. The ZFAT 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 ZFAT X1 and X3 variants were biallelically expressed in both bovine tissues and placentas. A 311 bp bovine ZFAT-AS1 complementary DNA (cDNA) sequence was obtained by aligning the human ZFAT-AS1 cDNA sequence with the bovine genome and conducting reverse transcription polymerase chain reaction amplification. Bovine ZFAT-AS1 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 ZFAT, 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}
引用次数: 0
Genomic responses to climatic challenges in beef cattle: A review. 肉牛基因组对气候挑战的响应:综述。
IF 1.8 3区 生物学
Animal genetics Pub Date : 2024-09-01 DOI: 10.1111/age.13474
Daniele Colombi, Francesco Perini, Stefano Bettini, Salvatore Mastrangelo, Fabio Abeni, Giuseppe Conte, Donata Marletta, Martino Cassandro, Umberto Bernabucci, Roberta Ciampolini, Emiliano Lasagna
{"title":"Genomic responses to climatic challenges in beef cattle: A review.","authors":"Daniele Colombi, Francesco Perini, Stefano Bettini, Salvatore Mastrangelo, Fabio Abeni, Giuseppe Conte, Donata Marletta, Martino Cassandro, Umberto Bernabucci, Roberta Ciampolini, Emiliano Lasagna","doi":"10.1111/age.13474","DOIUrl":"https://doi.org/10.1111/age.13474","url":null,"abstract":"<p><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":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Core competing endogenous RNA network based on mRNA and non-coding RNA expression profiles in chicken fatty liver 基于鸡脂肪肝中 mRNA 和非编码 RNA 表达谱的核心竞争性内源性 RNA 网络。
IF 1.8 3区 生物学
Animal genetics Pub Date : 2024-08-20 DOI: 10.1111/age.13469
Qingxing Xiao, Yonghong Zhang, Hongyu Ni, Yijing Yin, Anchong Gao, Benhai Cui, Wei Zhang, Yumei Li, Yuwei Yang
{"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}
引用次数: 0
Exonisation of an intronic L1 element in the dystrophin gene associated with X-linked muscular dystrophy in a Border Collie dog 与一只边境牧羊犬的 X 连锁肌营养不良症有关的肌营养不良蛋白基因中 L1 内含子元素的剥离。
IF 1.8 3区 生物学
Animal genetics Pub Date : 2024-08-17 DOI: 10.1111/age.13470
Mario Van Poucke, Liesbet Ledeganck, Ling T. Guo, G. Diane Shelton, Sofie F. M. Bhatti, Ine Cornelis, Luc Peelman
{"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}
引用次数: 0
A genome-wide association study reveals candidate genes and regulatory regions associated with birth weight in pigs 全基因组关联研究揭示了与猪出生体重相关的候选基因和调控区域。
IF 1.8 3区 生物学
Animal genetics Pub Date : 2024-08-13 DOI: 10.1111/age.13468
Dadong Deng, Hongtao Wang, Kun Han, Zhenshuang Tang, Xiaoping Li, Xiangdong Liu, Xiaolei Liu, Xinyun Li, Mei Yu
{"title":"A genome-wide association study reveals candidate genes and regulatory regions associated with birth weight in pigs","authors":"Dadong Deng,&nbsp;Hongtao Wang,&nbsp;Kun Han,&nbsp;Zhenshuang Tang,&nbsp;Xiaoping Li,&nbsp;Xiangdong Liu,&nbsp;Xiaolei Liu,&nbsp;Xinyun Li,&nbsp;Mei Yu","doi":"10.1111/age.13468","DOIUrl":"10.1111/age.13468","url":null,"abstract":"<p>Piglet birth weight is associated with preweaning survival, and its related traits have been included in the breeding program. Thus, understanding its genetic basis is essential. This study identified four birth weight-associated genomic regions on chromosomes 2, 4, 5, and 7 through genome-wide association study analysis in 7286 pigs from three different pure breeds using the FarmCPU model. The genetic and phenotypic variance explained by the four candidate regions is 8.42% and 1.85%, respectively. Twenty-eight candidate genes were detected, of which <i>APPL2</i>, <i>TGFBI</i>, <i>MACROH2A1</i>, and <i>SEC22B</i> have been reported to affect body growth or development. In addition, 21 H3K4me3-enriched peaks overlapped with the birth weight-associated genomic regions were identified by integrating the genome-wide association study results with our previous ChIP-seq and RNA-seq data generated in the pig placenta, a fetal organ relevant to birth weight, and three of the regulatory regions influence <i>TGFBI</i>, <i>MACROH2A1</i>, and <i>SEC22B</i> expression. This study provides new insights into understanding the mechanisms for birth weight. Further investigating the variants in the regulatory regions would help identify the functional variants for birth weight in pigs.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141970495","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}
引用次数: 0
Heterozygous DSP in-frame deletion in a poodle with syndromic ichthyosis involving additional hair and tooth abnormalities 一只贵宾犬患有综合鱼鳞病,并伴有额外的毛发和牙齿异常。
IF 1.8 3区 生物学
Animal genetics Pub Date : 2024-08-13 DOI: 10.1111/age.13467
Sarah Kiener, Georg Lehner, Vidhya Jagannathan, Monika Welle, Tosso Leeb
{"title":"Heterozygous DSP in-frame deletion in a poodle with syndromic ichthyosis involving additional hair and tooth abnormalities","authors":"Sarah Kiener,&nbsp;Georg Lehner,&nbsp;Vidhya Jagannathan,&nbsp;Monika Welle,&nbsp;Tosso Leeb","doi":"10.1111/age.13467","DOIUrl":"10.1111/age.13467","url":null,"abstract":"<p>Ichthyoses comprise a large heterogeneous group of skin disorders, characterized by generalized scaly and hyperkeratotic skin. We investigated a miniature poodle with early onset generalized scaling, dry and irregularly thickened skin, paw pad hyperkeratosis and abnormalities in hair and teeth. The clinical signs of ichthyosis were confirmed by histopathological examination, which revealed mild epidermal hyperplasia and lamellar orthokeratotic hyperkeratosis. A hereditary condition was suspected and a genetic investigation was initiated. We sequenced the whole genome of the affected dog and searched for potentially causative variants in functional candidate genes for the observed phenotype. The analysis revealed a heterozygous in-frame deletion in <i>DSP</i>, NC_049256.1:g.8804542_8804544del resulting from a de novo mutation event as evidenced by genotyping leukocyte DNA from both parents. The 3 bp deletion is predicted to remove one aspartic acid without disrupting the open reading frame (XM_038584124.1:c.1821_1823del, XP_038440052.1:p.(Asp608del)). The <i>DSP</i> gene encodes desmoplakin, a desmosomal plaque protein, responsible for cell–cell adhesion to provide resistance to mechanical stress in epidermal and cardiac tissues. We hypothesize that the deletion of one amino acid in the N-terminal globular head domain acts in a dominant negative manner and thus impairs the proper connection with other proteins. Several variants in <i>DSP</i> in humans and cattle have been described to result in different phenotypes associated with hair and skin abnormalities, sometimes in combination with variable cardiac and/or dental manifestations. In conclusion, we characterized a new syndromic ichthyosis phenotype in a dog and identified a de novo 3 bp deletion in the <i>DSP</i> gene as causal variant.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/age.13467","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141970496","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}
引用次数: 0
Integration of ssGWAS and ROH analyses for uncovering genetic variants associated with reproduction traits in Large White pigs 整合 ssGWAS 和 ROH 分析,发现与大白猪繁殖性状相关的遗传变异。
IF 1.8 3区 生物学
Animal genetics Pub Date : 2024-08-12 DOI: 10.1111/age.13465
Zhenyang Zhang, Wei Zhao, Zhen Wang, Yuchun Pan, Qishan Wang, Zhe Zhang
{"title":"Integration of ssGWAS and ROH analyses for uncovering genetic variants associated with reproduction traits in Large White pigs","authors":"Zhenyang Zhang,&nbsp;Wei Zhao,&nbsp;Zhen Wang,&nbsp;Yuchun Pan,&nbsp;Qishan Wang,&nbsp;Zhe Zhang","doi":"10.1111/age.13465","DOIUrl":"10.1111/age.13465","url":null,"abstract":"<p>The low heritability of reproduction traits such as total number born (TNB), number born alive (NBA) and adjusted litter weight until 21 days at weaning (ALW) poses a challenge for genetic improvement. In this study, we aimed to identify genetic variants that influence these traits and evaluate the accuracy of genomic selection (GS) using these variants as genomic features. We performed single-step genome-wide association studies (ssGWAS) on 17 823 Large White (LW) pigs, of which 2770 were genotyped by 50K single nucleotide polymorphism (SNP) chips. Additionally, we analyzed runs of homozygosity (ROH) in the population and tested their effects on the traits. The genomic feature best linear unbiased prediction (GFBLUP) was then carried out in an independent population of 350 LW pigs using identified trait-related SNP subsets as genomic features. As a result, our findings identified five, one and four SNP windows that explaining more than 1% of genetic variance for ALW, TNB, and NBA, respectively and discovered 358 hotspots and nine ROH islands. The ROH SSC1:21814570–27186456 and SSC11:7220366–14276394 were found to be significantly associated with ALW and NBA, respectively. We assessed the genomic estimated breeding value accuracy through 20 replicates of five-fold cross-validation. Our findings demonstrate that GFBLUP, incorporating SNPs located in effective ROH (<i>p</i>-value &lt; 0.05) as genomic features, might enhance GS accuracy for ALW compared with GBLUP. Additionally, using SNPs explaining more than 0.1% of the genetic variance in ssGWAS for NBA as genomic features might improve the GS accuracy, too. However, it is important to note that the incorporation of inappropriate genomic features can significantly reduce GS accuracy. In conclusion, our findings provide valuable insights into the genetic mechanisms of reproductive traits in pigs and suggest that the ssGWAS and ROH have the potential to enhance the accuracy of GS for reproductive traits in LW pigs.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141915958","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}
引用次数: 0
Genetic Eye Diseases in Animals: A Selected Review of Recent Advances 动物遗传性眼病:最新进展精选回顾》。
IF 1.8 3区 生物学
Animal genetics Pub Date : 2024-07-17 DOI: 10.1111/age.13460
A. M. Komáromy, J. A. Lenstra
{"title":"Genetic Eye Diseases in Animals: A Selected Review of Recent Advances","authors":"A. M. Komáromy,&nbsp;J. A. Lenstra","doi":"10.1111/age.13460","DOIUrl":"10.1111/age.13460","url":null,"abstract":"","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/age.13460","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141625787","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}
引用次数: 0
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