Animal genetics最新文献

{"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}

{"title":"Genomic characterization of dryland adaptation in endangered Anxi cattle in China","authors":"Yang Lyu,&nbsp;Tingting Yao,&nbsp;Zhefu Chen,&nbsp;Ruiyao Huangfu,&nbsp;Haijian Cheng,&nbsp;Weidong Ma,&nbsp;Xingshan Qi,&nbsp;Fuqiang Li,&nbsp;Ningbo Chen,&nbsp;Chuzhao Lei","doi":"10.1111/age.13416","DOIUrl":"10.1111/age.13416","url":null,"abstract":"<p>Local species exhibit distinctive indigenous characteristics while showing unique productive and phenotypic traits. However, the advent of commercialization has posed a substantial threat to the survival of indigenous species. Anxi cattle, an endangered native breed in China, have evolved unique growth and reproductive characteristics in extreme desert and semidesert ecosystems. In this study, we conducted a genomic comparison of 10 Anxi cattle genomes with those of five other global populations/breeds to assess genetic diversity and identify candidate genomic regions in Anxi cattle. Population structure and genetic diversity analyses revealed that Anxi cattle are part of the East Asian cattle clade, exhibiting higher genetic diversity than commercial breeds. Through selective sweep analysis, we identified specific genetic variations linked to the environmental adaptability of Anxi cattle. Notably, we identified several candidate genes, including <i>CERS3</i> involved in regulating skin permeability and antimicrobial functions, <i>RBFOX2</i> associated with cardiac development, <i>SLC16A7</i> participated in the regulation of pancreatic endocrine function, and <i>SPATA3</i> related to reproduction. Our findings revealed the distinctive genomic features of Anxi cattle in dryland environments, provided invaluable insights for further research and breed preservation, and had important significance for enriching the domestic cattle breeding gene bank.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"55 3","pages":"352-361"},"PeriodicalIF":2.4,"publicationDate":"2024-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140020811","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 mutation in CACNA1A is associated with autosomal dominant bovine familial convulsions and ataxia in Angus cattle","authors":"Rachel R. Reith,&nbsp;Jonathan E. Beever,&nbsp;Joe C. Paschal,&nbsp;Jason Banta,&nbsp;Brian F. Porter,&nbsp;David J. Steffen,&nbsp;Thomas B. Hairgrove,&nbsp;Jessica L. Petersen","doi":"10.1111/age.13409","DOIUrl":"10.1111/age.13409","url":null,"abstract":"<p>Bovine familial convulsions and ataxia (BFCA) is considered an autosomal dominant syndrome with incomplete penetrance. Nine Angus calves from the same herd were diagnosed with BFCA within days of birth. Necropsy revealed cerebellar and spinal cord lesions associated with the condition. Parentage testing confirmed that all affected calves had a common sire. The sire was then bred to 36 cows across two herds using artificial insemination, producing an additional 14 affected calves. The objective of this investigation was to identify hypothesized dominant genetic variation underlying the condition. Whole-genome sequencing was performed on the sire, six affected and seven unaffected paternal half-sibling calves and combined with data from 135 unrelated controls. The sire and five of the six affected calves were heterozygous for a nonsense variant (Chr7 g.12367906C&gt;T, c.5073C&gt;T, p.Arg1681*) in <i>CACNA1A.</i> The other affected calves (<i>N</i> = 8) were heterozygous for the variant but it was absent in the other unaffected calves (<i>N</i> = 7) and parents of the sire. This variant was also absent in sequence data from over 6500 other cattle obtained via public repositories and collaborator projects. The variant in <i>CACNA1A</i> is expressed in the cerebellum of the ataxic calves as detected in the transcriptome and was not differentially expressed compared with controls. The CACNA1A protein is part of a highly expressed cerebellar calcium voltage gated channel. The nonsense variant is proposed to cause haploinsufficiency, preventing proper transmission of neuronal signals through the channel and resulting in BFCA.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"55 3","pages":"344-351"},"PeriodicalIF":2.4,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/age.13409","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139995298","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 genetic variability of the host on the resistance to Neospora caninum infection in cattle","authors":"Anabella Dinon,&nbsp;Franco Fiorani,&nbsp;Lucía María Campero,&nbsp;Dadín Prando Moore,&nbsp;Pablo Marcelo Corva","doi":"10.1111/age.13410","DOIUrl":"10.1111/age.13410","url":null,"abstract":"<p><i>Neospora caninum</i> is one of the most frequently diagnosed abortifacient pathogens in cattle. There is abundant genomic information about the parasite itself, but very little is known about the genetic variability of resistance in the most common intermediate host. The aim of this review was to compile all the available information about the genetic variability associated with the resistance to <i>N. caninum</i> both between and within cattle breeds. We systematically searched for published studies that investigated the influence of genetics of the host on the prevalence of <i>N. caninum</i> and risk of abortion. Beyond the potential confounding effects of feeding systems, management and animal density, some lines of evidence suggest that Holstein, the most popular breed for milk production, has a comparatively higher risk of abortion due to infections by <i>N. caninum</i>, whereas some beef breeds from Continental Europe seem to be more resistant. It is still not clear if different genetic mechanisms of resistance are involved in the two known routes of infection: postnatal ingestion of oocysts or transplacental transmission from the infected dam to the fetus. Genomic information associated with susceptibility to infection and risk of abortion in different cattle breeds is still scarce. The information reported here could be useful to identify new research alternatives and to define novel strategies to deal with this major problem of animal production.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"55 3","pages":"304-318"},"PeriodicalIF":2.4,"publicationDate":"2024-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/age.13410","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139989128","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":"Evaluation of the effectiveness of single nucleotide polymorphisms compared to microsatellite markers for parentage verification in Moroccan horses","authors":"O. Aminou,&nbsp;B. Badaoui,&nbsp;M. Machmoum,&nbsp;M. Piro","doi":"10.1111/age.13408","DOIUrl":"10.1111/age.13408","url":null,"abstract":"<p>The International Society for Animal Genetics (ISAG) currently advocates for a transition towards single nucleotide polymorphism (SNP) markers as a potential alternative for equine parentage verification. To ascertain the efficacy of this transition, it is imperative to evaluate the performance of parentage testing using SNPs in juxtaposition with short tandem repeats (STRs). As per ISAG's recommendation, we used an equine genotyping-by-sequencing panel with 144 SNPs for this purpose. Equine parentage is currently realized using 16 microsatellites (STRs) excluding the LEX3 marker. In this study, 1074 horses were genotyped using the 144 SNPs panel, including 432 foals, 414 mares, and 228 stallions, from five different breeds: 293 Arabians, 167 Barbs, 189 Thoroughbreds, 73 Anglo-Arabians, and 352 Arabian-Barbs. As a result, two SNPs markers were eliminated from the panel system due to inconsistent amplification across all examined individuals leaving 142 SNPs markers for analysis. A comparative analysis between SNPs and STRs markers revealed that the mean expected heterozygosity was 0.457 for SNPs and 0.76 for STRs, while the mean observed heterozygosity stood at 0.472 for SNPs and 0.72 for STRs. Furthermore, the probability of identity was calculated to be 5.722 × 10⁻⁵⁷ for SNPs and 1.25 × 10⁻¹⁵ for STRs markers. In alignment with the Hardy–Weinberg equilibrium in polyploids test, 110 out of the total SNPs were consistent with the Hardy–Weinberg equilibrium in polyploids test (<i>p</i> &gt; 0.05). Employing both SNPs and STRs markers, the mean polymorphic information content was discerned to be 0.351 for SNPs and 0.72 for STRs. The cumulative exclusion probabilities for SNP markers exceeded 99.99%, indicating that the 142 SNPs panel might be adequate for parentage testing. In contrast, when utilizing STRs markers, the combined average exclusion probabilities for one and both parents were determined to be 99.8% and 99.9%, respectively. Our comprehensive study underscores the potential of SNPs in equine parentage verification, especially when compared to STRs in terms of exclusion probabilities. As a corollary, the application of SNPs for parentage verification and identification can significantly contribute to the conservation initiative for the five Moroccan horse breeds. Nonetheless, further research is required to address and replace the deficient SNPs within the panel.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"55 3","pages":"404-409"},"PeriodicalIF":2.4,"publicationDate":"2024-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139929652","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":"Phenotypic correlations of carpal gland diverticular number with production traits and its genome-wide association analysis in multiple pig populations","authors":"Dengshuai Cui,&nbsp;Longyun Li,&nbsp;Naibiao Yu,&nbsp;Sanya Xiong,&nbsp;Shijun Xiao,&nbsp;Hao Zheng,&nbsp;Zhiyong Huang,&nbsp;Yuanmei Guo,&nbsp;Lusheng Huang","doi":"10.1111/age.13407","DOIUrl":"10.1111/age.13407","url":null,"abstract":"<p>Pig carpal glands play crucial roles in territorial recognition, reproductive behavior, and information exchange; however, their effects on production traits and underlying genetic mechanisms remain unclear. In this study, 1028 pigs from six populations were counted for the carpal gland diverticular numbers (CGDNs) on the left (CGDN_L) and right (CGDN_R) legs, and their carcass and meat quality traits were assessed. The CGDNs were significantly different among the populations, and Licha Black pigs had a lower CGDN than the Bama Xiang breed. It was also significantly different between sexes, with males having more diverticula than females (<i>p</i> ≤ 0.0391). Moreover, the number was asymmetric, with CGDN_R being significantly higher than CGDN_L. Notably, CGDNs was significantly correlated with each other in phenotype and genetics and with 24-h pH, 24-h meat color score, 24-h marbling score, fat content, moisture content, sodium salt content, and saturated fatty acid content in phenotype. Furthermore, genome-wide association analyses identified seven SNPs in association with CGDNs at a 5% genome-wide significance level, all of which were located in a 1.78-Mb (35.347–37.129 Mb) region on chromosome 1. CNC10010837 and CNC10010840 were the top SNPs: both had an additive effect of 0.789 ± 0.120 on CGDN_R with <i>p</i> = 8.31E-10. These findings provide important insights into the functions and underlying genetic mechanisms of swine carpal glands.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"55 3","pages":"396-403"},"PeriodicalIF":2.4,"publicationDate":"2024-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139911905","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":"LncRNA ENSGALG00000021686 regulates fat metabolism in chicken hepatocytes via miR-146b/AGPAT2 pathway","authors":"Wenhao Xing,&nbsp;Shijie Li","doi":"10.1111/age.13405","DOIUrl":"10.1111/age.13405","url":null,"abstract":"<p>The liver contributes to lipid metabolism as the hub of fat synthesis. Long non-coding RNAs (lncRNAs) are considered the regulators of cellular processes. Since <i>LncRNA ENSGALG00000021686</i> (lncRNA 21 686) has been described as a regulator of lipid metabolism, the present study aimed to clarify the role of <i>lncRNA 21 686</i> in chicken hepatocytes’ lipid metabolism. Thirty-two chickens were divided into four groups and were treated with diets containing different amounts of fat, and the hepatic expression of <i>lncRNA 21 686</i> and miR-146b along with the levels of proteins involved in the regulation of fat metabolism, lipid indices and oxidative stress were measured. Moreover, primary chicken hepatocytes were transfected with <i>lncRNA 21 686</i> small interfering RNA or microRNA (miRNA, <i>miR</i>)<i>-146b</i> mimics to measure the consequences of suppressing lncRNA or inducing miRNA expression on the levels of proteins involved in fat metabolism and stress markers. The results showed that the high-fat diet modulated the expression of <i>lncRNA 21 686</i> and <i>miR-146b</i> (<i>p</i>-value &lt; 0.001). Moreover, there was a significant increase in 1-acyl-sn-glycerol-3-phosphate acyltransferase 2 (<i>AGPAT2</i>) gene expression and protein levels and modulated fat-related markers. Furthermore, the results showed that <i>lncRNA 21 686</i> suppression reduced the expression of <i>AGPAT2</i> and its downstream proteins (<i>p</i>-value &lt; 0.05). Overexpression of <i>miR-146b</i> regulated fat metabolism indicator expression. Transfection experiments revealed that <i>lncRNA 21 686</i> suppression increased <i>miR-146b</i> expression. The findings suggested a novel mechanism containing <i>lncRNA 21 686</i>/<i>miR-146b</i>/<i>AGPAT2</i> in the regulation of fat metabolism in chicken hepatocytes.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"55 3","pages":"420-429"},"PeriodicalIF":2.4,"publicationDate":"2024-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139899245","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}