Animal genetics最新文献

{"title":"Landmarks in the history of selective sweeps","authors":"Manjit Panigrahi,&nbsp;Divya Rajawat,&nbsp;Sonali Sonejita Nayak,&nbsp;Kanika Ghildiyal,&nbsp;Anurodh Sharma,&nbsp;Karan Jain,&nbsp;Chuzhao Lei,&nbsp;Bharat Bhushan,&nbsp;Bishnu Prasad Mishra,&nbsp;Triveni Dutt","doi":"10.1111/age.13355","DOIUrl":"10.1111/age.13355","url":null,"abstract":"<p>Half a century ago, a seminal article on the hitchhiking effect by Smith and Haigh inaugurated the concept of the selection signature. Selective sweeps are characterised by the rapid spread of an advantageous genetic variant through a population and hence play an important role in shaping evolution and research on genetic diversity. The process by which a beneficial allele arises and becomes fixed in a population, leading to a increase in the frequency of other linked alleles, is known as genetic hitchhiking or genetic draft. Kimura's neutral theory and hitchhiking theory are complementary, with Kimura's neutral evolution as the ‘null model’ and positive selection as the ‘signal’. Both are widely accepted in evolution, especially with genomics enabling precise measurements. Significant advances in genomic technologies, such as next-generation sequencing, high-density SNP arrays and powerful bioinformatics tools, have made it possible to systematically investigate selection signatures in a variety of species. Although the history of selection signatures is relatively recent, progress has been made in the last two decades, owing to the increasing availability of large-scale genomic data and the development of computational methods. In this review, we embark on a journey through the history of research on selective sweeps, ranging from early theoretical work to recent empirical studies that utilise genomic data.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"54 6","pages":"667-688"},"PeriodicalIF":2.4,"publicationDate":"2023-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10234253","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":"Genome-wide association study identifies variants associated with semen volume in white-feathered broilers","authors":"G. M. Zhang,&nbsp;P. H. Liu,&nbsp;L. Chen,&nbsp;J. M. Zheng,&nbsp;G. P. Zhao,&nbsp;W. H. Xing,&nbsp;J. Wen,&nbsp;Q. H. Li","doi":"10.1111/age.13358","DOIUrl":"10.1111/age.13358","url":null,"abstract":"<p>Semen is a measure of the reproductive efficiency of roosters, which affects the economic benefits of white-feathered broilers. Over the years, research in this field has mainly focused on hens, while there have been fewer studies on the reproductive traits of roosters. To identify the genes related to the semen traits of roosters, we used a chicken 55 K SNP chip to genetically type the white-feathered population (220) and performed imputation with resequencing data from 97 roosters. In total, 1 048 576 SNPs were obtained and used for genome-wide association analysis of semen volume, from which 197 genome-wide significant markers were identified, all within the interval of 13.82–16.12 Mb on chromosome 7. By combining our results with the biological functions of genes in the interval, four candidate genes were identified that potentially relate to semen volume: <i>FAPP1</i>, <i>OSBPL6</i>, <i>SESTD1</i> and <i>SSFA2</i>. Our findings may provide a basis for further research on the genetic mechanism and marker-assisted selection of semen volume in white-feathered broilers.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"54 6","pages":"803-807"},"PeriodicalIF":2.4,"publicationDate":"2023-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10580363","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":"Searching for new signals for susceptibility to umbilical hernia through genome-wide association analysis in three pig breeds","authors":"Hui Yang,&nbsp;Lei Wang,&nbsp;Lilin Yin,&nbsp;Zhenshuang Tang,&nbsp;Zhangxu Wang,&nbsp;Xiangdong Liu,&nbsp;Tao Xiang,&nbsp;Mei Yu,&nbsp;Xiaolei Liu,&nbsp;Changchun Li","doi":"10.1111/age.13347","DOIUrl":"10.1111/age.13347","url":null,"abstract":"<p>Umbilical hernia (UH) is a prevalent congenital disorder in pigs, resulting in considerable economic losses and severe animal welfare issues. In the present study, we conducted a genome-wide association study (GWAS) using the GeneSeek 50K Chip in 2777 pigs (Duroc, <i>n</i> = 1267; Landrace, <i>n</i> = 696; and Yorkshire, <i>n</i> = 814) to explore the candidate genes underlying the risk of umbilical hernia in pigs. After quality control analyses, 2748 animals and 48 524 single nucleotide polymorphisms (SNPs) were retained for subsequent GWAS analysis using the FarmCPU model. The heritability of umbilical hernias was estimated to 0.51 ± 0.04, indicating a reasonable basis for investigating genetic markers associated with this disorder. We identified 54 SNPs and 517 candidate genes that showed significant associations with susceptibility to umbilical hernia across the combined population of the three pig breeds. Gene enrichment analyses highlighted several crucial pathways for platelet degranulation, inflammatory mediator regulation of TRP channels and ion transport. These findings provide further insights into the underlying genetic architecture of umbilical hernias in pigs.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"54 6","pages":"798-802"},"PeriodicalIF":2.4,"publicationDate":"2023-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10598212","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 de novo 2.3 kb structural variant in MITF explains a novel splashed white phenotype in a Thoroughbred family","authors":"R. R. Bellone,&nbsp;J. Tanaka,&nbsp;E. Esdaile,&nbsp;R. B. Sutton,&nbsp;F. Payette,&nbsp;L. Leduc,&nbsp;B. J. Till,&nbsp;A. K. Abdel-Ghaffar,&nbsp;M. Hammond,&nbsp;K. G. Magdesian","doi":"10.1111/age.13352","DOIUrl":"10.1111/age.13352","url":null,"abstract":"<p>Splashed white in horses is characterized by extensive white patterning on the legs, face and abdomen and may be accompanied by deafness. To date, seven variants in <i>microphthalmia-associated transcription factor</i> (<i>MITF</i>) and two variants in <i>Paired Box 3</i> (<i>PAX3</i>) have been identified to explain this phenotype. A splashed white Thoroughbred stallion, whose sire and dam were not patterned, was hypothesized to have a <i>de novo</i> variant leading to his white coat pattern. A whole-genome sequencing candidate gene approach identified two single nucleotide variants (SNVs) in <i>SOX10</i>, four SNVs in <i>MITF</i> and a 2.3 kb deletion in <i>MITF</i> with the alternative allele present in this stallion but absent in the other 18 horses analyzed. All six SNVs were annotated as modifiers and were not further considered. The deletion in <i>MITF</i> (NC_009159.3:g.21555811_21558139delinsAAAT) encompasses exon 9 encoding a part of the helix–loop–helix domain required for DNA binding. Sanger sequencing and parentage testing confirmed that this deletion was a <i>de novo</i> mutation of maternal origin. Consistent with the published nomenclature, we denote this likely causal variant as SW8. Genotyping three of this stallion's offspring identified SW8 only in the nearly all-white foal that was confirmed deaf by brainstem auditory evoked response testing. This foal was also a compound heterozygote for dominant white variants (W20/W22), but to date, W variants alone have not been connected to deafness. SW8 marks the fourth de novo <i>MITF</i> variant in horses reported to cause white patterning. The link between deafness and all <i>MITF</i> variants with and without other variants impacting melanocyte development and function needs to be further explored.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"54 6","pages":"752-762"},"PeriodicalIF":2.4,"publicationDate":"2023-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10580420","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":"Candidate signatures of positive selection for environmental adaptation in indigenous African cattle: A review","authors":"Sumaya Kambal,&nbsp;Abdulfatai Tijjani,&nbsp;Sabah A. E. Ibrahim,&nbsp;Mohamed-Khair A. Ahmed,&nbsp;Joram M. Mwacharo,&nbsp;Olivier Hanotte","doi":"10.1111/age.13353","DOIUrl":"10.1111/age.13353","url":null,"abstract":"<p>Environmental adaptation traits of indigenous African cattle are increasingly being investigated to respond to the need for sustainable livestock production in the context of unpredictable climatic changes. Several studies have highlighted genomic regions under positive selection probably associated with adaptation to environmental challenges (e.g. heat stress, trypanosomiasis, tick and tick-borne diseases). However, little attention has focused on pinpointing the candidate causative variant(s) controlling the traits. This review compiled information from 22 studies on signatures of positive selection in indigenous African cattle breeds to identify regions under positive selection. We highlight some key candidate genome regions and genes of relevance to the challenges of living in extreme environments (high temperature, high altitude, high infectious disease prevalence). They include candidate genes involved in biological pathways relating to innate and adaptive immunity (e.g. <i>BoLAs</i>, <i>SPAG11</i>, <i>IL1RL2</i> and <i>GFI1B</i>), heat stress (e.g. <i>HSPs</i>, <i>SOD1</i> and <i>PRLH</i>) and hypoxia responses (e.g. <i>BDNF</i> and <i>INPP4A</i>). Notably, the highest numbers of candidate regions are found on BTA3, BTA5 and BTA7. They overlap with genes playing roles in several biological functions and pathways. These include but are not limited to growth and feed intake, cell stability, protein stability and sweat gland development. This review may further guide targeted genome studies aiming to assess the importance of candidate causative mutations, within regulatory and protein-coding genome regions, to further understand the biological mechanisms underlying African cattle's unique adaption.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"54 6","pages":"689-708"},"PeriodicalIF":2.4,"publicationDate":"2023-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10216128","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":"In Memoriam","authors":"","doi":"10.1111/age.13354","DOIUrl":"10.1111/age.13354","url":null,"abstract":"","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"54 5","pages":"587-590"},"PeriodicalIF":2.4,"publicationDate":"2023-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/age.13354","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10226756","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":"Development and validation of SNP markers for giant panda using a kompetitive allele specific PCR approach","authors":"Shujuan Ma,&nbsp;Ying Zhu,&nbsp;Honglin Wu","doi":"10.1111/age.13350","DOIUrl":"10.1111/age.13350","url":null,"abstract":"","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"54 5","pages":"659-661"},"PeriodicalIF":2.4,"publicationDate":"2023-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10229386","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":"DYRK1B haploinsufficiency in a Holstein cattle with epilepsy","authors":"Joana G. P. Jacinto,&nbsp;Marilena Bolcato,&nbsp;Irene M. Häfliger,&nbsp;Anna Oevermann,&nbsp;Arcangelo Gentile,&nbsp;Cord Drögemüller","doi":"10.1111/age.13348","DOIUrl":"10.1111/age.13348","url":null,"abstract":"<p>In this study, epilepsy with focal seizures progressing to generalized seizures was diagnosed in a 6-month-old Holstein heifer. The seizures were characterized by a brief pre-ictal phase with depression and vocalization. During the ictal phase eyelid spasms, tongue contractions, nodding and abundant salivation were observed, rapidly followed by a convulsive phase with bilateral tonic, clonic or tonic–clonic activity and loss of consciousness. Finally, during the postictal phase the heifer was obtunded and disorientated, unable to perceive obstacles and hypermetric, and pressed its head against objects. In the inter-seizure phase, the heifer was clinically normal. Neuropathology revealed axonal degeneration in the brainstem and diffuse astrocytic hypertrophic gliosis. Whole genome sequencing of the affected heifer identified a private heterozygous splice-site variant in <i>DYRK1B</i> (NM_001081515.1: c.-101-1G&gt;A), most likely resulting in haploinsufficiency owing to loss-of-function. This represents a report of a <i>DYRK1B</i>-associated disease in cattle and adds <i>DYRK1B</i> to the candidate genes for epilepsy.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"54 5","pages":"623-627"},"PeriodicalIF":2.4,"publicationDate":"2023-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/age.13348","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10238007","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":"Degree of leukochimerism with calf age in Angus-crossbred twin sets","authors":"Heather L. Hunt,&nbsp;Brian W. Kirkpatrick","doi":"10.1111/age.13349","DOIUrl":"10.1111/age.13349","url":null,"abstract":"<p>Twinning in cattle is infrequent and usually undesired. It can result in an increased occurrence of abortion and dystocia, reduced calf survival and a high likelihood of freemartinism in mixed-sex twins. Twin gestations are also commonly associated with the formation of placental vascular anastomoses (PVA) between twins. Through PVA they share blood, hormones (leading to freemartinism in mixed sex twins) and hematopoietic stem cells, which are the progenitors of white blood cells. The sharing of stem cells between twins can result in leukochimeric twin sets. These are twins that have white blood cells derived from both self and the co-twin owing to the fetal migration of hematopoietic stem cells from the extraembryonic mesoderm of the yolk sac to final sites like bone marrow and thymus. This study examined the degree to which this leukochimerism changes with age. DNA was extracted from hair bulbs containing mesenchymal dermal papilla to determine the individual's true genotype and blood samples were obtained at six time points from 1 week to 8 months of age to assess leukochimerism. Samples were genotyped using a medium density SNP chip, and quantitative estimates of allele frequency were determined using SNPs for which members of a twin set had alternative homozygous genotypes. The results indicate statistically significant changes in the proportion of self and co-twin with age and suggest that by 2–4 months of age the genotypic mix in white blood cells represents the hematopoetic stem cell population resident in the individual (i.e. permanently found in thymus and bone marrow).</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"54 5","pages":"619-622"},"PeriodicalIF":2.4,"publicationDate":"2023-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/age.13349","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10230121","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":"Exclusion of previously described variant in LTBP2 for primary glaucoma in Australian Burmese cats","authors":"J. Ranocchia,&nbsp;W. Irving,&nbsp;B. Haase","doi":"10.1111/age.13346","DOIUrl":"10.1111/age.13346","url":null,"abstract":"&lt;p&gt;Glaucoma is a diverse group of progressive neurodegenerative eye disorders that can lead to irreversible blindness (Davis et al., &lt;span&gt;2016&lt;/span&gt;; Maggio, &lt;span&gt;2015&lt;/span&gt;; Weinreb et al., &lt;span&gt;2014&lt;/span&gt;). Based on the underlying aetiology, glaucoma can be classified as either primary or secondary and within primary further categorised as open or closed angle. Both forms result in an increased intraocular pressure (IOP), and while secondary glaucoma is characterised by an increase in IOP due to pathological process such as inflammation, primary glaucoma lacks these distinguishable pathologies. Being one of the most common heritable disorders in humans, 112 genetic loci and variants in 74 genes have been identified as being associated with primary glaucoma to date (Gao et al., &lt;span&gt;2018&lt;/span&gt;; Khawaja et al., &lt;span&gt;2018&lt;/span&gt;; MacGregor et al., &lt;span&gt;2018&lt;/span&gt;; Wang et al., &lt;span&gt;2017&lt;/span&gt;, &lt;span&gt;2018&lt;/span&gt;). While less common, primary glaucoma has been described in dogs and cats (Hampson et al., &lt;span&gt;2002&lt;/span&gt;; Martin &amp; Wyman, &lt;span&gt;1978&lt;/span&gt;; Miller &amp; Bentley, &lt;span&gt;2015&lt;/span&gt;; Schallek et al., &lt;span&gt;2012&lt;/span&gt;), and, although rarely observed in cats, a breed predisposition has been reported in Burmese, Siamese, and Persian cats (Dietrich, &lt;span&gt;2005&lt;/span&gt;; Glaze, &lt;span&gt;2005&lt;/span&gt;).&lt;/p&gt;&lt;p&gt;To date, only one variant in &lt;i&gt;the Latent Transforming Growth Factor-β Binding Protein 2&lt;/i&gt; (&lt;i&gt;LTBP2&lt;/i&gt;) gene has been associated with primary glaucoma in domestic cats (Kuehn et al., &lt;span&gt;2016&lt;/span&gt;). The aim of this study was to assess for the presence of the previously described variant in Australian Burmese cats clinically diagnosed with primary glaucoma.&lt;/p&gt;&lt;p&gt;EDTA-stabilised whole blood from 10 Australian Burmese cats diagnosed with primary glaucoma at a specialist animal eye hospital in Sydney were collected and genomic DNA isolated using a standard phenol–chloroform extraction method. Genotypes for the &lt;i&gt;LTBP2&lt;/i&gt; variant were determined by PCR and direct sequencing of PCR products as described before (Gao et al., &lt;span&gt;2018&lt;/span&gt;). Sequence data were analysed using Sequencher 5.4.6 (GeneCodes) and compared to the feline &lt;i&gt;LTBP2&lt;/i&gt; reference sequence (XM_023255858.2) according to FelCat9.&lt;/p&gt;&lt;p&gt;Sequence data analysis demonstrated that none of the 10 affected Burmese cats carried the previously described 4-bp insertion in the &lt;i&gt;LTBP2&lt;/i&gt; gene (g.121929604_121929607insCCTC; according to FelCat9) and that all cases were homozygous for the wild-type allele at this position. As none of the cases investigated carried the previously described variant in &lt;i&gt;LTBP2&lt;/i&gt; (Kuehn et al., &lt;span&gt;2016&lt;/span&gt;), this variant can be excluded from being responsible for primary glaucoma in the investigated Burmese cats. Considering that the previously described variant in &lt;i&gt;LTBP&lt;/i&gt;2 has been identified in Siamese cats, another yet unknown genetic variant may be responsible for the observed phenotype in the Burmese cat. While &lt;i&gt;","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"54 5","pages":"657-658"},"PeriodicalIF":2.4,"publicationDate":"2023-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/age.13346","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10228808","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}