Animal genetics最新文献

{"title":"Identification of a global gene expression signature associated with the genetic risk of catastrophic fracture in iPSC-derived osteoblasts from Thoroughbred horses","authors":"Esther Palomino Lago,&nbsp;Amy K. C. Ross,&nbsp;Alyce McClellan,&nbsp;Deborah J. Guest","doi":"10.1111/age.13504","DOIUrl":"10.1111/age.13504","url":null,"abstract":"<p>Bone fractures are a significant problem in Thoroughbred racehorses. The risk of fracture is influenced by both genetic and environmental factors. To determine the biological processes that are affected in genetically susceptible horses, we utilised polygenic risk scoring to establish induced pluripotent stem cells (iPSCs) from horses at high and low genetic risk. RNA-sequencing on iPSC-derived osteoblasts revealed 112 genes that were significantly differentially expressed. Forty-three of these genes have known roles in bone, 27 are not yet annotated in the equine genome and 42 currently have no described role in bone. However, many of the proteins encoded by the known and unknown genes have reported interactions. Functional enrichment analyses revealed that the differentially expressed genes were overrepresented in processes regulating the extracellular matrix and pathways known to be involved in bone remodelling and bone diseases. Gene set enrichment analysis also detected numerous biological processes and pathways involved in glycolysis with the associated genes having a higher expression in the iPSC-osteoblasts from horses with low polygenic risk scores for fracture. Therefore, the differentially expressed genes may be relevant for maintaining bone homeostasis and contribute to fracture risk. A deeper understanding of the consequences of mis-regulation of these genes and the identification of the DNA variants which underpin their differential expression may reveal more about the molecular mechanisms which are involved in equine bone health and fracture risk.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"56 1","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11726005/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142969473","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":"Novel insights into sheep domestication in Southwest Asia based on genome-wide sequencing","authors":"Wenwen Fang,&nbsp;Hojjat Asadollahpour Nanaei,&nbsp;Yu Liu,&nbsp;Huanhuan Zhang,&nbsp;Lisheng Miao,&nbsp;Yang Cao,&nbsp;Haiguo Jin,&nbsp;Yang Cao","doi":"10.1111/age.13500","DOIUrl":"10.1111/age.13500","url":null,"abstract":"<p>The origin of domestic sheep (<i>Ovis aries</i>) can be traced back to the Asian mouflon (<i>Ovis gmelini</i>), in the Near East around 10 000 years ago. Genetic divergence within mouflon populations can occur due to factors such as geographical isolation, social structures, and environmental pressures, leading to different affinities with domestic sheep. However, few studies have reported the extent to which mouflon sheep contribute to domestic sheep in different regions. Here, we implemented the demographic analyses of sheep populations across the globe based on the whole genome resequencing data of 410 samples, Y chromosome genetic variation of 417 rams, and 396 complete mitogenomes of <i>O. aries</i>. This revealed genetic differentiation within Iranian mouflons and a close genetic affinity between northern Iranian mouflons and worldwide domestic populations. The result illustrates that domestic sheep in our study may have derived from the same mouflon populations. Furthermore, analyses of paternal and maternal genetic diversity showed that five Y chromosome haplogroups and seven mitochondrial haplogroups were identified, of which the lineages mtF and mtG were newly found and defined. A phylogeographic interpretation of our data reveals a cline of north to south Iranian mouflons, which may be largely explained by increasing urial introgression.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"56 1","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142942876","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":"Assessing genomic diversity and signatures of selection in Qingyuan Wapiti","authors":"Te Pi,&nbsp;Wenfeng Yi,&nbsp;Mingyue Hu,&nbsp;Xinjiao Quan,&nbsp;Laiming Tian,&nbsp;Hao Sun,&nbsp;Shouqing Yan","doi":"10.1111/age.13505","DOIUrl":"10.1111/age.13505","url":null,"abstract":"<p>Red deer is a species of family Cervidae that is widely distributed in the world and is often raised to provide antlers, as a trophy or traditional medicine materials, and meat. Currently, the whole genomic data for red deer are very limited. Qingyuan Wapiti (QYW), China's first breed of red deer by artificial breeding, is well known for its high yield of antlers and large body size. The phylogenetic tree showed that QYW had a closer genetic relationship with Tarim red deer than European red deer. To explore the genetic diversity and selection signatures, the whole genome of 28 QYW individuals was sequenced, and 19 401 749 biallelic SNPs and 1 849 784 indels were obtained. The value of observed heterozygosity, expected heterozygosity, and nucleotide diversity were 0.258598, 0.268844, and 0.002193, respectively. Based on Tajima's <i>D</i> and integrated haplotype score analyses, the candidate regions containing 187 genes were detected, including <i>PLD1</i>, <i>ANTXR1</i>, <i>PLCL1</i>, <i>CPE</i>, and <i>CTNNA3</i>, which have been reported to be correlated with osteogenesis and mineralization, growth, and body size by previous studies. The results obtained in this study will contribute to elucidating the genetic mechanisms underlying the formation of excellent traits in QYW and provide the whole genome data for future exploration of genomic diversity and adaptation evolution of red deer worldwide.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"56 1","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142942874","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":"Unexpected recombination at the polled locus in a horned Holstein calf from the mating of a homozygous polled sire and a heterozygous polled cow","authors":"Bertram Brenig","doi":"10.1111/age.13507","DOIUrl":"10.1111/age.13507","url":null,"abstract":"<p>In this study, I report an unexpected case of a Holstein calf that developed horns even though the sire was homozygous and the dam was heterozygous for polledness. After verifying and confirming the correct parentage, the parents and offspring were genotyped with the Illumina EuroG_MD BeadChip and the SNPs in the polled region on chromosome 1 were evaluated. In addition, the father was sequenced with next generation sequencing to identify possible, previously unknown variants. The deletion of two base pairs within the causative 80-kb duplication described for the Friesian polled variant was verified by melting curve analysis and the 80-kb duplication by droplet digital PCR. Analysis of all data showed that, as expected, the calf was heterozygous for all SNP positions flanking the 80-kb duplication but was homozygous wild type in the 80-kb duplication region and therefore carried horns. This is certainly a very rare case of a recombination within the highly conserved polled region, which on the one hand confirms that only the 80-kb duplication is responsible for the expression of the Friesian polled variant, but on the other hand also shows that caution is required when interpreting the usual routine genotyping of the horn status based on linked single nucleotide polymorphisms in the polled region on chromosome 1. Based on the present case, it is recommended that, in addition to the evaluation of the SNP data of the BeadChip, an extended diagnosis with direct detection of the 2-bp deletion (1:g.2629156_2629158delGT) should be carried out in any case when detecting the Friesian polled variant.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"56 1","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11707570/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142942877","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":"Single-step genome-wide association study reveals candidate genes for body mass index trait in Yunong-black pigs","authors":"Ziyi Wu,&nbsp;Tengfei Dou,&nbsp;Jiahao Wu,&nbsp;Liyao Bai,&nbsp;Yongqian Zhang,&nbsp;Shengyuan Zan,&nbsp;Songbai Yang,&nbsp;Hao Zhou,&nbsp;Jinyi Han,&nbsp;Xuelei Han,&nbsp;Ruimin Qiao,&nbsp;Kejun Wang,&nbsp;Feng Yang,&nbsp;Xin-Jian Li,&nbsp;Xiu-Ling Li","doi":"10.1111/age.13501","DOIUrl":"10.1111/age.13501","url":null,"abstract":"<p>Body mass index (BMI) can serve as a reasonable indicator of overall body fat content in pigs. This study aimed to identify underlying variants and candidate genes associated with BMI in Yunong-black pigs. A single-step genome-wide association analysis (GWAS) was performed on 1405 BMI records and 924 Yunong-black pigs genotyped using a 50 K SNP Chip. De-regressed estimated breeding values were taken as the response variable in the GWAS. The estimated heritability for BMI was 0.157. Nine significant regions were associated with BMI, accounting for 12.828% of genetic variance, with the highest region explaining 1.969% of the genetic variance. Linkage disequilibrium analysis of the nine significant regions revealed that SNPs in six single-step GWAS-identified genomic regions were all located in the linkage disequilibrium blocks. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses of the 29 protein-coding genes annotated to these regions revealed that <i>FABP2</i>, a key gene associated with BMI in human, was enriched in the fatty acid binding term and the fat digestion and absorption pathway. This study provides a better insight into the genetic architecture of the BMI trait, and offers potential molecular markers for the breeding of Yunong-black pigs.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"56 1","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142880923","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 TYR-iffic discovery: Identification of a second TYR variant associated with acromelanism in dogs","authors":"Samantha L. Van Buren,&nbsp;Anushka Panjwani,&nbsp;Carrie J. Finno","doi":"10.1111/age.13496","DOIUrl":"10.1111/age.13496","url":null,"abstract":"","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"56 1","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142875731","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":"Analysis of SLICK allele in African taurine and Zebu cattle breeds","authors":"Samrawit Gebeyehu,&nbsp;Bradley Heins,&nbsp;Tad Sonstegard,&nbsp;Johann Sölkner,&nbsp;Gábor Mészáros,&nbsp;Amadou Traoré,&nbsp;Albert Soudré","doi":"10.1111/age.13499","DOIUrl":"10.1111/age.13499","url":null,"abstract":"&lt;p&gt;The SLICK trait enhances heat tolerance by modifying physiological traits, such as improving sweating ability, and is phenotypically expressed as short and sleek coats (Davis et al., &lt;span&gt;2016&lt;/span&gt;; Olson et al., &lt;span&gt;2003&lt;/span&gt;). The SLICK coat trait in cattle is attributed to six naturally occurring truncation mutations in the prolactin receptor (PRLR) gene on bovine chromosome 20 (Flórez et al., &lt;span&gt;2020&lt;/span&gt;; Sosa et al., &lt;span&gt;2021&lt;/span&gt;). This results in frameshift mutations in the PRLR gene, particularly in exons 10 and 11, which disrupt the open reading frame, and leads to truncated receptor proteins that confer the SLICK phenotype (Davis et al., &lt;span&gt;2017&lt;/span&gt;; Porto-Neto et al., &lt;span&gt;2018&lt;/span&gt;). These mutations have been identified in many South American breeds, such as Senepol, Carora and Limonero, and the trait is inherited in an autosomal-dominant manner (Flórez et al., &lt;span&gt;2020&lt;/span&gt;; Flórez Murillo et al., &lt;span&gt;2024&lt;/span&gt;; Nicholas et al., &lt;span&gt;2024&lt;/span&gt;; Olson et al., &lt;span&gt;2003&lt;/span&gt;). The mutation was first identified in Criollo breeds: the Mexican Criollo Lechero has SLICK3 and SLICK4 at frequencies of 0.9 and 0.03; the Colombian Blanco Orejineg has SLICK1 and SLICK5 at frequencies of 0.50 and 0.38; and the Hartón del Valle has SLICK1, SLICK2, SLICK5 and SLICK6 at frequencies of 0.29, 0.18, 0.24 and 0.21 respectively (Flórez et al., &lt;span&gt;2020&lt;/span&gt;). Although the allelic frequency of the mutation is relatively low in some Criollo breeds, the autosomal-dominant inheritance pattern ensures that individuals carrying at least one copy of a SLICK allele exhibit the phenotype.&lt;/p&gt;&lt;p&gt;The SLICK allele is well documented in Criollo breeds of the Caribbean Basin, descended from Iberian taurine cattle (Flórez et al., &lt;span&gt;2020&lt;/span&gt;; Porto-Neto et al., &lt;span&gt;2018&lt;/span&gt;). The allele may also exist in African breeds because these cattle have environmental stressors similar to those of Criollo breeds. However, the specific SLICK mutation in African taurine cattle has not been identified (Xia et al., &lt;span&gt;2023&lt;/span&gt;). Although African cattle possess various tropical adaptations, it is unknown whether they exhibit the SLICK phenotype. Investigation of the presence and frequency of SLICK alleles in West African breeds is crucial for understanding the origins of these mutations and their potential application in breeding programs to enhance adaptability, productivity and resilience in tropical dairy systems. The study evaluated SLICK-causing mutations in African breeds compared with Criollo breeds. No SLICK mutations were found in a panel of 1063 genomic DNA samples from 40 breeds across 15 ecotypes, including 126 African taurine samples (Sonstegard et al., &lt;span&gt;2025&lt;/span&gt;). Genotyping of SLICK mutations (1–5) was done with iPlex assays (Geneseek, Lincoln, NE, USA). Allele frequencies were determined for four Criollo breeds (Mexican Criollo Lechero tropical, &lt;i&gt;n&lt;/i&gt; = 20; Colombian Blanco Orejinegro, &lt;i&gt;n&lt;/i","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"56 1","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11664028/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142875732","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":"Genome sequencing and assembly of feral chickens in the wild of Sulawesi, Indonesia","authors":"Hidayat Ashari,&nbsp;Li-Sheng Liu,&nbsp;Muhammad Ihsan Andi Dagong,&nbsp;Zheng-Fei Cai,&nbsp;Guo-Li Xie,&nbsp;Ting-Ting Yin,&nbsp;Ya-Ping Zhang,&nbsp;Jian-Lin Han,&nbsp;Min-Sheng Peng","doi":"10.1111/age.13497","DOIUrl":"10.1111/age.13497","url":null,"abstract":"<p>The feralization of domestic chicken makes the conservation and management of red jungle fowl (<i>Gallus gallus</i>) more complicated and challenging. We collected two Sulawesi feral chickens, located east of the Wallace Line, for whole-genome sequencing and de novo genome assembly. Phylogenetic and <i>f4</i>-statistics analyses indicated that the Sulawesi feralized domestic chickens (<i>G. g. domesticus</i>) received gene flow from <i>G. g. gallus</i>. We integrated ~45× ultra-long Oxford Nanopore Technology reads and ~28× PacBio HiFi reads to generate a de novo genome assembly of a female Sulawesi feral chicken (GGsula) with a contig N50 of 19.88 Mbp. We characterized structural variations in GGsula, and found some were related to nervous system. Our study provides the first genome assembly of feral chickens, which is a unique genomic resource to explore the process of chicken domestication and feralization.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"56 1","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142875776","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 genomic landscape of short tandem repeats in cattle","authors":"Pengfei Wang,&nbsp;Xin Sheng,&nbsp;Xiaoting Xia,&nbsp;Fuwen Wang,&nbsp;Ruizhe Li,&nbsp;Zulfiqar Ahmed,&nbsp;Ningbo Chen,&nbsp;Chuzhao Lei,&nbsp;Zhijie Ma","doi":"10.1111/age.13498","DOIUrl":"10.1111/age.13498","url":null,"abstract":"<p>Short tandem repeats (STRs) are abundant and have high mutation rates across cattle genomes; however, comprehensive exploration of cattle STRs is needed. Here, we constructed a comprehensive map of 467 553 polymorphic STRs (pSTRs) constructed from 423 cattle genomes representing 59 breeds worldwide. We observed that pSTRs in coding sequences and 5′UTRs (Untranslated Regions) were under strong selective constraints and exhibited a relatively low level of diversity. Furthermore, we found that these pSTRs underwent more contraction than expansion. Population analysis showed a strong positive correlation (<i>R</i> = 1) between pSTR diversity and single nucleotide polymorphic heterozygosity. We also investigated STR differences between taurine and indicine cattle and detected 2301 highly divergent STRs, which might relate to immune, endocrine and neurodevelopmental pathways. In summary, our large-scale study characterizes the spectrum of STRs in cattle, expands the scale of known cattle STR variation and provides novel insights into differences among various cattle subspecies.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"56 1","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142845648","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 3-bp deletion in the SLC45A2 gene is associated with loss of fleece pigmentation in black-fleeced Suffolk sheep","authors":"R. G. Tearle,&nbsp;T. Chen,&nbsp;F. D. Brien","doi":"10.1111/age.13495","DOIUrl":"10.1111/age.13495","url":null,"abstract":"<p>Sheep have naturally pigmented wool which interferes with dyeing. Selection has been carried out over many years to remove pigment, with substantial success, but most wool still contains some pigment. As an alternative to selection, it has been proposed to take a naturally occurring mutation found in black Suffolk sheep, that blocks wool pigmentation, and introgress it into other breeds. However, the nature of the mutation has not been identified, prompting us to characterise it. The Suffolk white-fleece phenotype is associated with a novel 3-bp deletion in the gene <i>SLC45A2</i>, which encodes a membrane bound transporter that mediates melanin synthesis. The deletion results in the removal of one amino acid from the protein. The assignment of this deletion as the likely causative mutation is supported by it: being homozygous in the genome of nine animals with a white fleece and not homozygous in the genomes of eight animals with a black fleece; having a high level of conservation of the encoded amino acid sequence in the region surrounding the deleted amino acid across Mammalia; and the same deletion (but in a compound heterozygous state) being found in human <i>SLC45A2</i> in a person with albinism.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"56 1","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142749754","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}