Animal genetics最新文献

{"title":"Identification of candidate genes associated with milk production and mastitis based on transcriptome-wide association study","authors":"Sevda Hosseinzadeh,&nbsp;Seyed Abbas Rafat,&nbsp;Arash Javanmard,&nbsp;Lingzhao Fang","doi":"10.1111/age.13422","DOIUrl":"10.1111/age.13422","url":null,"abstract":"<p>Genetic research for the assessment of mastitis and milk production traits simultaneously has a long history. The main issue that arises in this context is the known existence of a positive correlation between the risk of mastitis and lactation performance due to selection. The transcriptome-wide association study (TWAS) approach endeavors to combine the expression quantitative trait loci and genome-wide association study summary statistics to decode complex traits or diseases. Accordingly, we used the <span>farmgtex</span> project results as a complete <span>bovine</span> database for mastitis and milk production. The results of colocalization and TWAS approaches were used for the detection of functional associated candidate genes with milk production and mastitis traits on multiple tissue-based transcriptome records. Also, we used the <span>david</span> database for gene ontology to identify significant terms and associated genes. For the identification of interaction networks, the <span>genemania</span> and <span>string</span> databases were used. Also, the available <i>z</i>-scores in TWAS results were used for the calculation of the correlation between tissues. Therefore, the present results confirm that <i>LYNX1</i>, <i>DGAT1</i>, <i>C14H8orf33</i>, and <i>LY6E</i> were identified as significant genes associated with milk production in eight, six, five, and five tissues, respectively. Also, <i>FBXL6</i> was detected as a significant gene associated with mastitis trait. <i>CLN3</i> and <i>ZNF34</i> genes emerged via both the colocalization and TWAS approaches as significant genes for milk production trait. It is expected that TWAS and colocalization can improve our perception of the potential health status control mechanism in high-yielding dairy cows.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"55 3","pages":"430-439"},"PeriodicalIF":2.4,"publicationDate":"2024-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140580514","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":"The landscape of allelic expression and DNA methylation at the bovine SGCE/PEG10 locus","authors":"Yinjiao Zhang,&nbsp;Cui Zhang,&nbsp;Weina Chen,&nbsp;Haonan Huo,&nbsp;Shujing Li,&nbsp;Wenli Yu,&nbsp;Lanjie Jin,&nbsp;Kun Wang,&nbsp;Shijie Li","doi":"10.1111/age.13429","DOIUrl":"10.1111/age.13429","url":null,"abstract":"<p>Genomic imprinting is an epigenetic regulation in mammals in which a small subset of genes is monoallelically expressed dependent on their parental origin. A large imprinted domain, <i>SGCE/PEG10</i> locus, is located on human chromosome 7q21s and mouse proximal chromosome 6. However, genomic imprinting of bovine <i>SGCE/PEG10</i> cluster has not been systematically studied. In this study, we investigated allele expression of 14 genes of the <i>SGCE/PEG10</i> locus in bovine somatic tissues and term placenta using a single nucleotide polymorphism (SNP)-based sequencing method. In addition to <i>SGCE</i> and <i>PEG10</i>, two conserved paternally expressed genes in human and mice, five other genes (<i>TFPI2</i>, <i>GNG11</i>, <i>ASB4</i>, <i>PON1</i>, and <i>PON3</i>) were paternally expressed. Three genes, <i>BET1</i>, <i>COL1A2</i>, and <i>CASD1</i>, exhibited tissue-specific monoallelic expression. <i>CALCR</i> showed monoallelic expression in tissues but biallelic expression in the placenta. Three genes, <i>GNGT1</i>, <i>PPP1R9A</i>, and <i>PON2</i>, showed biallelic expression in cattle. Five differentially methylated regions (DMRs) were found to be associated with the allelic expression of <i>TFPI2</i>, <i>COL1A2</i>, <i>SGCE/PEG10</i>, <i>PON3</i>, and <i>ASB4</i> genes, respectively. The <i>SGCE/PEG10</i> DMR is a maternally hypermethylated germline DMR, but <i>TFPI2</i>, <i>COL1A2</i>, <i>PON3</i>, and <i>ASB4</i> DMRs are secondary DMRs. In summary, we identified five novel bovine imprinted genes (<i>GNG11</i>, <i>BET1</i>, <i>COL1A2</i>, <i>CASD1</i>, and <i>PON1</i>) and four secondary DMRs at the <i>SGCE/PEG10</i> locus.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"55 3","pages":"452-456"},"PeriodicalIF":2.4,"publicationDate":"2024-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140580595","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 novel QTL region for pH and meat color in Duroc pigs","authors":"Eduard Molinero,&nbsp;Ramona N. Pena,&nbsp;Joan Estany,&nbsp;Roger Ros-Freixedes","doi":"10.1111/age.13426","DOIUrl":"10.1111/age.13426","url":null,"abstract":"<p>One of the most important processes that occur during the transformation of muscle to meat is the pH decline as a consequence of the post-mortem metabolism of muscle tissue. Abnormal pH declines lead to pork defects such as pale, soft, and exudative meat. There is genetic variance for ultimate pH and the role of some genes on this phenotype is well established. After conducting a genome-wide association study on ultimate pH using 526 purebred Duroc pigs, we identified associated regions on <i>Sus scrofa</i> chromosomes (SSC) 3, 8, and 15. Functional candidate genes in these regions included <i>PRKAG3</i> and <i>PHKG1</i>. The SSC8 region, at 71.6 Mb, was novel and, although no candidate causative gene could be identified, it may have regulatory effects. Subsequent analysis on 828 pigs from the same population confirmed the impact of the three associated regions on pH and meat color. We detected no interaction between the three regions. Further investigations are necessary to unravel the functional significance of the novel genomic region at SSC8. These variants could be used as markers in marker-assisted selection for improving meat quality.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"55 3","pages":"465-470"},"PeriodicalIF":2.4,"publicationDate":"2024-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/age.13426","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140580792","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":"Study on the origin of the Baise horse based on whole-genome resequencing","authors":"Xiaoran Lin,&nbsp;Mo Feng,&nbsp;Ying Li,&nbsp;Yu Liu,&nbsp;Min Wang,&nbsp;Yuanyuan Li,&nbsp;Tao Yang,&nbsp;Chunjiang Zhao","doi":"10.1111/age.13424","DOIUrl":"10.1111/age.13424","url":null,"abstract":"<p>The Baise horse, an indigenous horse breed mainly distributed in the Baise region of Guangxi province in southwest China, has a long history as draft animal. However, there is a lack of research regarding the origin and ancestral composition of the Baise horse. In this study, whole-genome resequencing data from 236 horses of seven Chinese indigenous horse breeds, five foreign horse breeds, and four Przewalski's horses were used to investigate the relationships between the Baise horse and other horse breeds. The results showed that foreign horse breeds had no significant impact on the formation of the Baise horse. The two southwestern horse populations, the Debao pony and the Jinjiang horse, exhibit the closest genetic affinity with the Baise horse. This is consistent with their adjacent geographical distribution. Analysis of the migration route revealed a gene flow from the Chakouyi horse into the Baise horse. In summary, our results confirm that the formation of the Baise horse did not involve participation from foreign breeds. Geographical distance emerges as a crucial factor in determining the genetic relationships with the Baise horse. Gene flows of indigenous horse breeds along ancient routes of trade activities had played a role in the formation of the Baise horse.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"55 3","pages":"410-419"},"PeriodicalIF":2.4,"publicationDate":"2024-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140580605","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":"Whole-genome resequencing uncovers diversity and selective sweep in Kazakh cattle","authors":"Lei Xu,&nbsp;Yunyun Zhang,&nbsp;Yang Guo,&nbsp;Qiuming Chen,&nbsp;Menghua Zhang,&nbsp;Hong Chen,&nbsp;Juan Geng,&nbsp;Xixia Huang","doi":"10.1111/age.13425","DOIUrl":"10.1111/age.13425","url":null,"abstract":"<p>The Kazakh cattle in the Xinjiang Uygur Autonomous Region of China are highly adaptable and have multiple uses, including milk and meat production, and use as draft animals. They are an excellent original breed that could be enhanced by breeding and hybrid improvement. However, the genomic diversity and signature of selection underlying the germplasm characteristics require further elucidation. Herein, we evaluated 26 Kazakh cattle genomes in comparison with 103 genomes of seven other cattle breeds from regions around the world to assess the Kazakh cattle genetic variability. We revealed that the relatively low linkage disequilibrium at large SNP distances was strongly correlated with the largest effective population size among Kazakh cattle. Using population structural analysis, we next demonstrated a taurine lineage with restricted <i>Bos indicus</i> introgression among Kazakh cattle. Notably, we identified putative selected genes associated with resistance to disease and body size within Kazakh cattle. Together, our findings shed light on the evolutionary history and breeding profile of Kazakh cattle, as well as offering indispensable resources for germplasm resource conservation and crossbreeding program implementation.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"55 3","pages":"377-386"},"PeriodicalIF":2.4,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140334451","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":"Heterozygous ASPRV1 frameshift variant in a Pembroke Welsh Corgi with ichthyosis","authors":"Sarah Kiener,&nbsp;Susanne Åhman,&nbsp;Robert Cikota,&nbsp;Vidhya Jagannathan,&nbsp;Sohvi Blatter,&nbsp;Iva Cvitas,&nbsp;Sara Soto,&nbsp;Tosso Leeb","doi":"10.1111/age.13423","DOIUrl":"10.1111/age.13423","url":null,"abstract":"&lt;p&gt;Ichthyoses comprise a large, heterogeneous group of inherited cornification disorders. They are characterized by generalized scaly and hyperkeratotic skin (Oji et al., &lt;span&gt;2010&lt;/span&gt;). In humans, over 69 genes have been associated with different forms of ichthyosis, grouped into non-syndromic ichthyoses with the phenotypic expression of the disorder only seen in the skin, and syndromic ichthyoses that show additional organ involvement (Gutiérrez-Cerrajero et al., &lt;span&gt;2023&lt;/span&gt;; Uitto et al., &lt;span&gt;2020&lt;/span&gt;). Further subdivision into epidermolytic and non-epidermolytic ichthyoses is based on the presence or absence of light microscopic findings of vacuoles and lysis of keratinocytes (Mauldin, &lt;span&gt;2013&lt;/span&gt;). In dogs, several breed-specific ichthyoses have been described, and, to date, causal variants in nine different genes have been identified (Affolter et al., &lt;span&gt;2022&lt;/span&gt;; Bauer et al., &lt;span&gt;2017&lt;/span&gt;; Briand et al., &lt;span&gt;2019&lt;/span&gt;; Casal et al., &lt;span&gt;2017&lt;/span&gt;; Credille et al., &lt;span&gt;2005&lt;/span&gt;, &lt;span&gt;2009&lt;/span&gt;; Grall et al., &lt;span&gt;2012&lt;/span&gt;; Kiener et al., &lt;span&gt;2022&lt;/span&gt;; Kiener, Åhman, et al., &lt;span&gt;2023&lt;/span&gt;; Kiener, Castilla, et al., &lt;span&gt;2023&lt;/span&gt;; Metzger et al., &lt;span&gt;2015&lt;/span&gt;). These genes are mainly involved in the biosynthesis, metabolism, and transport of lipids required for skin barrier function or the intracellular protein network responsible for the integrity of skin structure (Gutiérrez-Cerrajero et al., &lt;span&gt;2023&lt;/span&gt;).&lt;/p&gt;&lt;p&gt;A 6-month-old Pembroke Welsh Corgi was presented with non-pruritic severe scaling (large 5–10-mm scales; Figure 1a), hyperkeratotic paw pads (Figure 1b), and fish-skin like flakes and erythema in friction areas (Figure 1c), present since shortly after birth. Histological examination of biopsies taken from haired skin and paw pads showed prominent compact to lamellar orthokeratotic hyperkeratosis (Figure 1d). The observed changes were compatible with non-epidermolytic ichthyosis.&lt;/p&gt;&lt;p&gt;We performed Illumina short-read whole-genome sequencing at 26× coverage on genomic DNA isolated from leukocytes to investigate potential causal genetic variants. The data were processed as previously described (Jagannathan et al., &lt;span&gt;2019&lt;/span&gt;) with respect to the genome reference assembly UU_Cfam_GSD_1.0. Subsequent comparison of the whole-genome sequencing data of the affected dog to 960 genetically diverse canine genomes (Table S1) revealed 76 heterozygous and eight homozygous protein-changing private variants (Table S2). Among them was a heterozygous two base-pair deletion variant in the ichthyosis candidate gene &lt;i&gt;ASPRV1&lt;/i&gt;, XM_038551592.1:c.594_595del or Chr10:NC_049231.1:69888722_69888723del, leading to a frameshift and altering 48% of the wildtype protein sequence, XP_038407520.1:p.(Leu199Argfs*342). The predicted mutant protein contains 539 compared to 381 amino acids in the wildtype protein. &lt;i&gt;ASPRV1&lt;/i&gt; encodes the retroviral-like aspartic protease 1, which","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"55 3","pages":"490-492"},"PeriodicalIF":2.4,"publicationDate":"2024-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/age.13423","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140317717","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":"Population structure and genomic diversity of the Einsiedler horse","authors":"Annik Gmel,&nbsp;Anne Ricard,&nbsp;Vinzenz Gerber,&nbsp;Markus Neuditschko","doi":"10.1111/age.13421","DOIUrl":"10.1111/age.13421","url":null,"abstract":"<p>The breeding history of the Einsiedler horse is closely connected with the Benedictine cloister Einsiedeln. In the mid-nineteenth century, it was decided to use European Warmblood stallions for cross-breeding and to abandon the selection of stallions. Since that time, it has only been possible to trace back the origin of Einsiedler horses using maternal ancestry information. Here, we collected high-density genotype data for European Warmblood horses (Selle Français, Swiss Warmblood and Einsiedler) and Franches-Montagnes horses, the last native Swiss horse breed, to unravel the current population structure of the Einsiedler horse. Using commonly applied methods to ascertain fine-scale population structures, it was not possible to clearly differentiate the Einsiedler from other European Warmblood horses. However, by means of runs of homozygosity (ROH) we were able to detect breed-specific ROH islands for the Einsiedler horse, including genes involved in domestication and adaptation to high altitude. Therefore, future breeding activities should involve the screening of these breed-specific ROH segments, the revival of cryopreserved sperm and the selection of Einsiedler stallions.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"55 3","pages":"475-479"},"PeriodicalIF":2.4,"publicationDate":"2024-03-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/age.13421","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140193140","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":"Domenico Bernoco: In Memorium","authors":"Doug Antczak,&nbsp;Harris Lewin,&nbsp;Marietta Bernoco,&nbsp;Ernest Bailey","doi":"10.1111/age.13418","DOIUrl":"10.1111/age.13418","url":null,"abstract":"","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"55 3","pages":"301-303"},"PeriodicalIF":2.4,"publicationDate":"2024-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/age.13418","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140179179","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":"Identification of polymorphic markers for germplasm conservation of three precious Chinese palace goldfish using whole-genome sequencing","authors":"Yuwei Huang,&nbsp;Aiying Cao,&nbsp;Beiyuan Zhang,&nbsp;Sen Li,&nbsp;Chuan He,&nbsp;Jian Gao,&nbsp;Xiaojuan Cao","doi":"10.1111/age.13419","DOIUrl":"10.1111/age.13419","url":null,"abstract":"<p>China was the first country in the world to breed goldfish and has generated many unique goldfish varieties, including the most aristocratic Chinese palace goldfish. Due to the lack of scientific research on Chinese palace goldfish, their selection and breeding are mainly carried out through traditional hybridization, leading to serious inbreeding and the degradation of germplasm resources. To this end, whole-genome resequencing was performed to understand the genetic variation among three different varieties (eggpompons, goosehead, and tigerhead) from nine core conserved populations in China. A total of 15 polymorphic SSRs were developed for population genetics, and all tested populations were considered moderately polymorphic with an average polymorphism information content value of 0.4943. Genetic diversity in different varieties showed that all conserved populations were well protected with the potential for continued exploitation. This study provides reliable molecular tools and a basis for designing conservation and management programs in Chinese palace goldfish.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"55 3","pages":"484-489"},"PeriodicalIF":2.4,"publicationDate":"2024-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140157410","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":"Unraveling genomic diversity and positive selection signatures of Qaidam cattle through whole-genome re-sequencing","authors":"Xudong Wei,&nbsp;Shuang Li,&nbsp;Huixuan Yan,&nbsp;Shengmei Chen,&nbsp;Ruizhe Li,&nbsp;Weizhong Zhang,&nbsp;Shengyu Chao,&nbsp;Weixing Guo,&nbsp;Wenhao Li,&nbsp;Zulfiqar Ahmed,&nbsp;Chuzhao Lei,&nbsp;Zhijie Ma","doi":"10.1111/age.13417","DOIUrl":"10.1111/age.13417","url":null,"abstract":"<p>Qaidam cattle are a typical Chinese native breed inhabiting northwest China. They bear the characteristics of high cold and roughage tolerance, low-oxygen adaptability and good meat quality. To analyze the genetic diversity of Qaidam cattle, 60 samples were sequenced using whole-genome resequencing technology, along with 192 published sets of whole-genome sequencing data of Indian indicine cattle, Chinese indicine cattle, North Chinese cattle breeds, East Asian taurine cattle, Eurasian taurine cattle and European taurine cattle as controls. It was found that Qaidam cattle have rich genetic diversity in <i>Bos taurus</i>, but the degree of inbreeding is also high, which needs further protection. The phylogenetic analysis, principal component analysis and ancestral component analysis showed that Qaidam cattle mainly originated from East Asian taurine cattle. Qaidam cattle had a closer genetic relationship with the North Chinese cattle breeds and the least differentiation from Mongolian cattle. Annotating the selection signals obtained by composite likelihood ratio, nucleotide diversity analysis, integrated haplotype score, genetic differentiation index, genetic diversity ratio and cross-population extended haplotype homozygosity methods, several genes associated with immunity, reproduction, meat, milk, growth and adaptation showed strong selection signals. In general, this study provides genetic evidence for understanding the germplasm characteristics of Qaidam cattle. At the same time, it lays a foundation for the scientific and reasonable protection and utilization of genetic resources of Chinese local cattle breeds, which has great theoretical and practical significance.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"55 3","pages":"362-376"},"PeriodicalIF":2.4,"publicationDate":"2024-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140118587","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}