Animal genetics最新文献

{"title":"genomeprofile: Unveiling the genomic profile for livestock breeding through comprehensive SNP array-based genotyping","authors":"Ina Hulsegge,&nbsp;Aniek C. Bouwman,&nbsp;Martijn F. L. Derks","doi":"10.1111/age.13466","DOIUrl":"10.1111/age.13466","url":null,"abstract":"<p>In livestock breeding, single nucleotide polymorphism arrays have become a cornerstone of modern livestock breeding. SNP arrays facilitate the identification of genetic markers linked to economically important traits and provide a powerful tool for predicting breeding values. However, conventional breeding programs often overlook additional genomic features contained in the SNP array data that can provide valuable insights into the genetic diversity, copy number variation, inbreeding levels and potential challenges in breeding lines. Here we present <span>genomeprofile</span>, a tool using SNP array-based genomic data, offering a comprehensive profile of breeding animals including the identification of copy number variants and runs of homozygosity, and screening for aneuploidy. By integrating these features into the breeding landscape, <span>genomeprofile</span> enables a more comprehensive picture of genomic variation, ultimately enhancing precision breeding strategies. To illustrate the practicality and efficacy of <span>genomeprofile</span>, we applied the tool to a dataset of four pig breeding lines. The <span>genomeprofile</span> tool is a user-friendly tool that processes genotype data in <span>finalreport</span> or <span>plink</span> ped format efficiently into useful output. The output contains copy number variations, runs of homozygosity, selection signatures, aneuploidy and inbreeding per individual and across populations. This allows breeding companies and researchers to identify unique individuals or regions in the genome of interest based on routinely collected data.</p>","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.13466","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141632376","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":"Multiomic meta-analysis suggests a correlation between steroid hormone-related genes and litter size in goats","authors":"Cheng-Li Liu,&nbsp;Hui-Long Mou,&nbsp;Ri-Su Na,&nbsp;Xiao Wang,&nbsp;Peng-Fei Hu,&nbsp;Simone Ceccobelli,&nbsp;Yong-Fu Huang,&nbsp;Guang-Xin E","doi":"10.1111/age.13464","DOIUrl":"10.1111/age.13464","url":null,"abstract":"<p>Litter size is a key indicator of production performance in livestock. However, its genetic basis in goats remains poorly understood. In this work, a genome-wide selection sweep analysis (GWSA) on 100 published goat genomes with different litter rates was performed for the first time to identify candidate genes related to kidding rate. This analysis was combined with the public RNA-sequencing data of ovary tissues (follicular phase) from high- and low-yielding goats. A total of 2278 genes were identified by GWSA. Most of these genes were enriched in signaling pathways related to ovarian follicle development and hormone secretion. Moreover, 208 differentially expressed genes between groups were obtained from the ovaries of goats with different litter sizes. These genes were substantially enriched in the cholesterol and steroid synthesis signaling pathways. Meanwhile, the weighted gene co-expression network was used to perform modular analysis of differentially expressed genes. The results showed that seven modules were reconstructed, of which one module showed a very strong correlation with litter size (<i>r</i> = −0.51 and <i>p-</i>value &lt;0.001). There were 51 genes in this module, and 39 hub genes were screened by Pearson's correlation coefficient between core genes &gt; 0.4, correlation coefficient between module members &gt; 0.80 and intra-module connectivity ≥5. Finally, based on the results of GWSA and hub gene Venn analysis, seven key genes (<i>ACSS2</i>, <i>HECW2</i>, <i>KDR</i>, <i>LHCGR</i>, <i>NAMPT</i>, <i>PTGFR</i> and <i>TFPI</i>) were found to be associated with steroid synthesis and follicle growth development. This work contributes to understanding of the genetic basis of goat litter size and provides theoretical support for goat molecular breeding.</p>","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":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141632377","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":"EquCab_Finn: A new reference genome assembly for the domestic horse, Finnhorse","authors":"Kisun Pokharel,&nbsp;Melak Weldenegodguad,&nbsp;Tiina Reilas,&nbsp;Juha Kantanen","doi":"10.1111/age.13463","DOIUrl":"10.1111/age.13463","url":null,"abstract":"<p>Finnhorse is Finland's native and national horse breed and it has genetic affinities to northern European and Asian horses. It has historical importance for agriculture, forest work and transport and as a war horse. Finnhorse has four breeding sections in the studbook and is under conservation and characterisation efforts. We sequenced and annotated the genome of a Finnhorse mare from the working horse section using PacBio and Omni-C data. This genome can complement the existing Thoroughbred reference genome (EquCab 3.0) and facilitate genetic studies of horses from northern Eurasia. We assembled 2.4 Gb of the genome with an N50 scaffold length of 83.8 Mb and the genome annotation resulted in a total of 19 748 protein coding genes of which 1200 were Finnhorse specific. The assembly has high quality and synteny with the current horse reference genome. We manually curated five genes of interest and deposited the final assembly in the European Nucleotide Archive under the accession no. PRJEB71364.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/age.13463","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141578755","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":"Genomic analysis links the American mink Royal pastel coat phenotype to retroviral element type 1 insertion in the HPS3 gene","authors":"Andrey D. Manakhov,&nbsp;Nelli A. Aarakelyan,&nbsp;Adela V. Lapteacru,&nbsp;Tatiana V. Andreeva,&nbsp;Oleg V. Trapezov,&nbsp;Evgeny I. Rogaev","doi":"10.1111/age.13461","DOIUrl":"10.1111/age.13461","url":null,"abstract":"<p>To date, only 10 of the more than 30 fur colours that had been observed in American mink (<i>Neogale vison</i>) have been linked to specific genes. The Royal pastel fur colour is part of a large family of brownish colours that are quite similar to one another, making breeding and selecting processes more difficult. Here we carried out whole-genome sequencing of five American minks with Royal pastel (<i>b</i>/<i>b</i>) phenotypes originating from two distinct mink populations. We identified an insertion of endogenous retroviral element type 1 (ERV1) into the first intron of the gene encoding the HPS3 protein, which regulates the trafficking of tyrosinase-containing vesicles to maturing melanosomes. With Cas9-targeted nanopore sequencing, we reconstructed the full-length sequence of the 11.7 Kb ERV1 insertion and observed hypermethylation that spread to the <i>HPS3</i> gene promoter region. These findings highlight the role of HPS3 in the formation of melanosomes and melanin, as well as the genetic process regulating the intensity and spectrum of hair colour. Moreover, in mink breeding projects, these data are also useful for tracking economically important fur qualities.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141490538","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":"Construction of a high-density linkage map and QTL detection for growth traits in South African abalone (Haliotis midae)","authors":"Thendo Stanley Tshilate,&nbsp;Edson Ishengoma,&nbsp;Clint Rhode","doi":"10.1111/age.13462","DOIUrl":"10.1111/age.13462","url":null,"abstract":"<p><i>Haliotis midae</i> is one of the most important molluscs in South African commercial aquaculture. In this study, a high-resolution integrated linkage map was constructed, and QTL identified using 2b-RADseq for genotyping SNPs in three families. The final integrated linkage map was composed by merging the individual family maps, resulting in 3290 informative SNPs mapping to 18 linkage groups, conforming to the known haploid chromosome number for <i>H. midae</i>. The total map spanned 1798.25 cM with an average marker interval of 0.55 cM, representing a genome coverage of 98.76%. QTL analysis, across all three families, resulted in a total of five QTL identified for growth-related traits, shell width, shell length, and total body weight. For shell width and total body weight, one QTL was identified for each trait respectively, whilst three QTL were identified for shell length. The identified QTL respectively explained between 7.20% and 11.40% of the observed phenotypic variance. All three traits were significantly correlated (<i>r</i> = 0.862–0.970; <i>p</i> &lt; 0.01) and shared overlapping QTL. The QTL for growth traits were mapped back to the <i>H. midae</i> draft genome and BLAST searches revealed the identity of candidate genes, such as <i>egf-1</i>, <i>megf10</i>, <i>megf6</i>, <i>tnx</i>, <i>sevp1</i>, <i>kcp</i>, <i>notch1</i>, and s<i>cube2</i> with possible functional roles in <i>H. midae</i> growth. The constructed high-density linkage map and mapped QTL have given valuable insights regarding the genetic architecture of growth-related traits and will be important genetic resources for marker-assisted selection. It remains, however, important to validate causal variants through linkage disequilibrium fine mapping in future.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/age.13462","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141465711","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":"A metagenomic survey of the fecal microbiome of the African savanna elephant (Loxodonta africana)","authors":"Louis Lategan du Preez,&nbsp;Elzette van der Walt,&nbsp;Angel Valverde,&nbsp;Christopher Rothmann,&nbsp;Frederick Wilhelm Cornelius Neser,&nbsp;Errol Duncan Cason","doi":"10.1111/age.13458","DOIUrl":"10.1111/age.13458","url":null,"abstract":"<p>The African savanna elephant (<i>Loxodonta africana</i>) is the largest terrestrial animal on Earth and is found primarily in Southern and Eastern Africa. It is a hindgut, colonic fermenter and subsists on a diet of raw plant materials found in its grazing area. In this study the bacterial, archaeal and fungal populations of seven African savanna elephant fecal metagenomes were first characterized using amplicon sequencing. On the genus level it was observed that the p-1088-a5 gut group in the bacteriome, <i>Methanocorpusulum</i> and <i>Methanobrevibacter</i> in the archaeome and <i>Alternaria</i>, <i>Aurobasidium</i>, <i>Didymella</i> and <i>Preussia</i> in the mycome, predominated. Subsequently, metagenomic shotgun sequencing was employed to identify possible functional pathways and carbohydrate-active enzymes (CAZymes). Carbohydrate catabolic pathways represented the main degradation pathways, and the fecal metagenome was enriched in the glycohydroside (GH) class of CAZymes. Additionally, the top GH families identified – GH43, GH2, GH13 and GH3 – are known to be associated with cellulytic, hemicellulytic and pectolytic activities. Finally, the CAZymes families identified in the African savanna elephant were compared with those found in the Asian elephant and it was demonstrated that there is a unique repository of CAZymes that could be leveraged in the biotechnological context such as the degradation of lignocellulose for the production of second-generation biofuels and energy.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/age.13458","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141454673","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":"A single base pair duplication in the SLC33A1 gene is associated with fetal losses and neonatal lethality in Manech Tête Rousse dairy sheep","authors":"Maxime Ben Braiek,&nbsp;Soline Szymczak,&nbsp;Céline André,&nbsp;Philippe Bardou,&nbsp;Francis Fidelle,&nbsp;Itsasne Granado-Tajada,&nbsp;Florence Plisson-Petit,&nbsp;Julien Sarry,&nbsp;Florent Woloszyn,&nbsp;Carole Moreno-Romieux,&nbsp;Stéphane Fabre","doi":"10.1111/age.13459","DOIUrl":"10.1111/age.13459","url":null,"abstract":"<p>We recently discovered that the Manech Tête Rousse (MTR) deficient homozygous haplotype 2 (MTRDHH2) probably carries a recessive lethal mutation in sheep. In this study, we fine-mapped this region through whole-genome sequencing of five MTRDHH2 heterozygous carriers and 95 non-carriers from various ovine breeds. We identified a single base pair duplication within the <i>SLC33A1</i> gene, leading to a frameshift mutation and a premature stop codon (p.Arg246Alafs*3). SLC33A1 encodes a transmembrane transporter of acetyl-coenzyme A that is crucial for cellular metabolism. To investigate the lethality of this mutation in homozygous MTR sheep, we performed at-risk matings using artificial insemination (AI) between heterozygous <i>SLC33A1</i> variant carriers (<i>SLC33A1_dupG</i>). Pregnancy was confirmed 15 days post-AI using a blood test measuring interferon Tau-stimulated MX1 gene expression. Ultrasonography between 45 and 60 days post-AI revealed a 12% reduction in AI success compared with safe matings, indicating embryonic/fetal loss. This was supported by the <i>MX1</i> differential expression test suggesting fetal losses between 15 and 60 days of gestation. We also observed a 34.7% pre-weaning mortality rate in 49 lambs born from at-risk matings. Homozygous <i>SLC33A1_dupG</i> lambs accounted for 47% of this mortality, with deaths occurring mostly within the first 5 days without visible clinical signs. Therefore, appropriate management of <i>SLC33A1_dupG</i> with an allele frequency of 0.04 in the MTR selection scheme would help increase overall fertility and lamb survival.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/age.13459","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141454674","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":"Dissecting loci that underpin the genetic correlations between production, fertility, and urea traits in Australian Holstein cattle","authors":"Babatunde S. Olasege,&nbsp;Irene van den Berg,&nbsp;Mekonnen Haile-Mariam,&nbsp;Phuong N. Ho,&nbsp;Zhen Yin Oh,&nbsp;Laercio R. Porto-Neto,&nbsp;Ben J. Hayes,&nbsp;Jennie E. Pryce,&nbsp;Marina R. S. Fortes","doi":"10.1111/age.13455","DOIUrl":"10.1111/age.13455","url":null,"abstract":"<p>Unfavorable genetic correlations between milk production, fertility, and urea traits have been reported. However, knowledge of the genomic regions associated with these unfavorable correlations is limited. Here, we used the correlation scan method to identify and investigate the regions driving or antagonizing the genetic correlations between production vs. fertility, urea vs. fertility, and urea vs. production traits. Driving regions produce an estimate of correlation that is in the same direction as the global correlation. Antagonizing regions produce an estimate in the opposite direction of the global estimates. Our dataset comprised 6567, 4700, and 12,658 Holstein cattle with records of production traits (milk yield, fat yield, and protein yield), fertility (calving interval) and urea traits (milk urea nitrogen and blood urea nitrogen predicted using milk-mid-infrared spectroscopy), respectively. Several regions across the genome drive the correlations between production, fertility, and urea traits. Antagonizing regions were confined to certain parts of the genome and the genes within these regions were mostly involved in preventing metabolic dysregulation, liver reprogramming, metabolism remodeling, and lipid homeostasis. The driving regions were enriched for QTL related to puberty, milk, and health-related traits. Antagonizing regions were mostly related to muscle development, metabolic body weight, and milk traits. In conclusion, we have identified genomic regions of potential importance for dairy cattle breeding. Future studies could investigate the antagonizing regions as potential genomic regions to break the unfavorable correlations and improve milk production as well as fertility and urea traits.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/age.13455","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141417355","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":"Neuronal ceroid lipofuscinosis in a Schapendoes dog is caused by a missense variant in CLN6","authors":"Kim K. L. Bellamy,&nbsp;Fredrik S. Skedsmo,&nbsp;Josefin Hultman,&nbsp;Johan Høgset Jansen,&nbsp;Frode Lingaas","doi":"10.1111/age.13457","DOIUrl":"10.1111/age.13457","url":null,"abstract":"<p>Neuronal ceroid lipofuscinosis (NCL) is a group of neurodegenerative disorders that occur in humans, dogs, and several other species. NCL is characterised clinically by progressive deterioration of cognitive and motor function, epileptic seizures, and visual impairment. Most forms present early in life and eventually lead to premature death. Typical pathological changes include neuronal accumulation of autofluorescent, periodic acid-Schiff- and Sudan black B-positive lipopigments, as well as marked loss of neurons in the central nervous system. Here, we describe a 19-month-old Schapendoes dog, where clinical signs were indicative of lysosomal storage disease, which was corroborated by pathological findings consistent with NCL. Whole genome sequencing of the affected dog and both parents, followed by variant calling and visual inspection of known NCL genes, identified a missense variant in <i>CLN6</i> (c.386T&gt;C). The variant is located in a highly conserved region of the gene and predicted to be harmful, which supports a causal relationship. The identification of this novel <i>CLN6</i> variant enables pre-breeding DNA-testing to prevent future cases of NCL6 in the Schapendoes breed, and presents a potential natural model for NCL6 in humans.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/age.13457","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141309468","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":"Independent CHRNE mutations at serine 503 in English Springer Spaniels and a Smooth Fox Terrier having congenital myasthenic syndrome","authors":"Erin Peterson,&nbsp;Tori E. Rudolph,&nbsp;Alison Starr-Moss,&nbsp;Kendall Anderson,&nbsp;Vanda A. Lennon,&nbsp;G. Diane Shelton,&nbsp;Leigh Anne Clark","doi":"10.1111/age.13456","DOIUrl":"10.1111/age.13456","url":null,"abstract":"<p>Congenital myasthenic syndromes (CMSs) are inherited disorders of neuromuscular transmission. In the 1980s, spontaneously occurring CMS following autosomal recessive inheritance patterns were described in English Springer Spaniels (ESSs) (Oda et al., <span>1984</span>) and Smooth Fox Terriers (SFTs) (Miller et al., <span>1983</span>; OMIA:000685–9615). Affected puppies exhibited muscle weakness and fatigability that was exacerbated by exercise. Skeletal muscle biopsies revealed notably fewer acetylcholine receptors (AChRs) than healthy controls, and no autoantibodies against AChR were detected. Ohno et al. (<span>2023</span>) describe 35 genes classified into 14 groups according to the pathomechanical, clinical, and therapeutic features of human CMS patients. Forms of CMS with AChR deficiency most often result from mutation of <i>CHRNE</i>, encoding the epsilon subunit of the AChR (Finsterer, <span>2019</span>). Homozygous mutations in other subunits are typically embryonic lethal (Engel et al., <span>2015</span>). To identify the genetic cause for CMS in these breeds, we sequenced the coding regions and splice sites of <i>CHRNE</i>.</p><p>We obtained archival thymus tissue from two affected ESS half-siblings, peripheral blood leukocytes from their unaffected dam (an obligate carrier), and cultured muscle cells from an affected SFT. Buccal swabs were collected from 17 unaffected, unrelated ESSs with informed owner consent under protocols approved by the Clemson University Institutional Review Board (IBC2015-24). DNA was extracted following Puregene Kit protocols (Qiagen). PCR amplification and sequencing of <i>CHRNE</i> exons 3–13 were conducted for the affected individuals and obligate carrier as described in Rinz et al., <span>2015</span>. Based on updated gene annotation (XM_014113502.3), we designed new primers to capture exons 1 and 2: exon 1 forward 5′-GAATCATCGGTGGAATCTGT-3′ and reverse 5′-GGAGTAGAAATGAGAGGGACC-3′, exon 2 forward 5′-CAATGATGAGTTTTCTGGGTG-3′ and reverse 5′-CCAATCACACCAGCAGAGTC-3′. Resultant sequences were compared to the canFam4 reference genome.</p><p>In both breeds, we discovered unique point mutations at position chr5:31915101 in exon 13. A C&gt;A transversion in the ESS predicts the substitution of an arginine for a serine (S503R) (XP_013968977.2). A rapid genotyping protocol was developed through restriction enzyme digestion using Hinf1 (Fisher BioReagents), following manufacturer's instructions. PCR products from exons 12 and 13 incubated with Hinf1 resulted in distinct banding patterns corresponding to genotype when resolved on an agarose gel (Figure S1). All 17 healthy ESSs produced a single 612-bp band. The two affected ESSs produced bands at 398 and 214 bp, and the obligate carrier had all three fragment sizes.</p><p>In the affected SFT, we identified a 1-bp insertion (c.1508_1509insG) that predicts a frameshift mutation, p.Ser503Argfs*14. The ESS and SFT variants were absent from 1987 dog genomes available thr","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/age.13456","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141295405","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}