Animal genetics最新文献

{"title":"Comparative genomics reveals common diversity and adaptation to harsh environments in the Arabian Peninsula indigenous chickens","authors":"Abdulwahad Assiri,&nbsp;Adriana Vallejo-Trujillo,&nbsp;Mohammed Al-Abri,&nbsp;Hussain Bahbahani,&nbsp;Faisal Almathen,&nbsp;Abulgasim Ahbara,&nbsp;Waleed Al Marzooqi,&nbsp;Abdulfatai Tijjani,&nbsp;Raman Lawal,&nbsp;Olivier Hanotte","doi":"10.1111/age.70014","DOIUrl":"https://doi.org/10.1111/age.70014","url":null,"abstract":"<p>Identifying genomic regions under selection is crucial for comprehending the evolutionary history of the domestic chicken. Arabian Peninsula (AP) indigenous chickens are mostly found outdoors, being reared alongside other livestock for production purposes. These birds show high resilience to extreme temperatures (hot and cold), typical of the desert environment. The selection pressures responsible for unique local adaptations in these birds remain largely unidentified. Here, we aimed to investigate the genome diversity and structure of 15 indigenous chicken populations including 13 populations from the AP (<i>n</i> = 5), Ethiopia (<i>n</i> = 6), and the People's Republic of China (<i>n</i> = 2). We also included two commercial chicken populations, Fayoumi (selected for heat tolerance) and Chantecler (known for its cold tolerance). Principal component (PC) analysis separated all the populations based on their geographic areas of origin. PC1 separates the Ethiopian populations from the Chinese and AP populations, while PC2 separates the AP populations from the Chantecler, and the Ethiopian populations from the Dulong and Chantecler. The genome-wide signatures of analyses identified many candidate regions under positive selection. They include genes that may be associated with thermotolerance. These are involved in energy balance and metabolism (<i>SUGCT</i>, <i>HECW1</i>, <i>MMADHC</i>), cells apoptosis (<i>APP</i>, <i>SRBD1</i>, <i>NTN1</i>, <i>PUF60</i>, <i>SLC26A8</i>, <i>DAP</i>, <i>SUGCT</i>), angiogenesis (<i>RYR2</i>, <i>LDB2</i>, <i>SOX5</i>), skin protection to solar radiation (<i>FZD10</i>, <i>BCO2</i>, <i>WNT5B</i>, <i>COL6A2</i>, <i>SIRT1</i>) as well as growth (<i>NELL1</i>). Our findings suggest that Arabian chicken populations have a distinct gene pool polymorphism in relation to their adaptation to the harsh climatic environments of the AP.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"56 3","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/age.70014","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143897153","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":"Differences in allele frequencies of personality-related genes in three varieties of Shiba Inu in Japan","authors":"Minori Arahori,&nbsp;Yuki Matsumoto,&nbsp;Noriyoshi Akiyama,&nbsp;Miho Inoue-Murayama","doi":"10.1111/age.70012","DOIUrl":"https://doi.org/10.1111/age.70012","url":null,"abstract":"<p>Shiba Inu is a Japanese dog breed that originally functioned as a hunting dog but is now widely kept as a pet. This study conducted whole genome sequencing on two varieties of Shiba Inu, Mino-Shiba and San'in-Shiba, which are believed to strongly retain the hunting function, and compared them with the common pet Shiba Inu. The results showed that populations of the three varieties formed distinct clusters. We calculated the <i>F</i>_ST values for each site between each of the two varieties and identified genomic regions with significant differences that might affect function. <i>LRRTM4</i> and <i>OXTR</i> found in previous studies on dogs related to personality traits are indicated in this study, and <i>KIF27</i>, associated with Williams syndrome in humans, was also suggested to potentially influence hunting traits. This study highlights the unique genetic lineage of regional Shiba varieties compared to the commonly kept pet Shiba Inu, and provides a foundation for further research into how these genetic differences may affect current personality traits.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"56 3","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143871871","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 FAM8A1 frameshift variant is associated with REM sleep behavior disorder, urinary retention, and mydriasis in Russian Blue cats","authors":"Kimberley Stee,&nbsp;Mario Van Poucke,&nbsp;Jaume Alomar Huguet,&nbsp;Martí Pumarola Batlle,&nbsp;Kenny Bossens,&nbsp;Ariel Cohen-Solal,&nbsp;Leen Van Brantegem,&nbsp;Kaatje Kromhout,&nbsp;Sofie F. M. Bhatti,&nbsp;Luc Peelman,&nbsp;Ine Cornelis","doi":"10.1111/age.70013","DOIUrl":"https://doi.org/10.1111/age.70013","url":null,"abstract":"<p>REM sleep behavior disorder (RBD) is a disease characterized by the loss of lower motor neuron inhibition responsible for skeletal muscle atonia during REM sleep. It has been reported in humans, dogs and cats, and can be idiopathic or secondary to a neurodegenerative disease. Five young adult Russian Blue cats from two related families were presented for progressively worsening RBD episodes frequently associated with urinary loss. Three of these cats also suffered urinary retention with overflow incontinence between RBD episodes. Neurological examination revealed a large bladder in three cats and a bilateral mydriasis with absent pupillary light reflexes in two cats; further examinations were unremarkable. Treatment attempts were unsatisfactory, with four cats being euthanized. Histopathology of the brain did not reveal any abnormalities. A disease-associated 23-bp deletion in exon 1 of <i>FAM8A1</i> (NC_058372.1:g.11622168_11622190del), introducing a frameshift at codon 162 and a premature stop codon at codon 276 (XM_019831563.3:c.485_507del p.(Gln162Profs*115)), was identified by whole genome sequencing. The variant segregated in the affected families with a recessive mode of inheritance, showed an allele frequency of 1.5% in West-European Russian Blue cats (<i>N</i> = 68) and was not present in 276 cats belonging to 32 other breeds (including the closely related Nebelung breed). The variant FAM8A1 isoform is predicted to affect the assembly and activity of the endoplasmic reticulum-associated protein degradation pathway, which plays an important role in cell homeostasis. RBD and urinary retention syndrome is a hereditary encephalopathy affecting Russian Blue cats. A genetic test now allows diagnosis and prevention of this debilitating disease.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"56 3","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143861835","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":"Genetic and functional validation of CTSS in regulating intramuscular fat content of Duroc–Landrace–Yorkshire pigs","authors":"Ye Tian,&nbsp;Yuelei Zhao,&nbsp;Yao Yao,&nbsp;Mengting Li,&nbsp;Lifan Zhang,&nbsp;Wei Wei,&nbsp;Jie Chen","doi":"10.1111/age.70010","DOIUrl":"https://doi.org/10.1111/age.70010","url":null,"abstract":"<p>Intramuscular fat (IMF) is an important meat quality trait and a key target for molecular breeding in pigs. Our previous genome-wide association study identified SNP rs80931414 (A&gt;G) as a significant site associated with IMF content. In this study, we further performed genotyping and association analysis of SNP rs80931414 within a Duroc–Landrace–Yorkshire (DLY) pig population. We found that the IMF content in pigs with AA genotype was significantly higher than that in those with GG genotype. SNP rs80931414 is a genetic variation in <i>CTSS</i>, therefore we hypothesized that <i>CTSS</i> is a candidate gene for IMF content trait in DLY pig and conducted research on gene function of <i>CTSS</i>. Our results indicated that both the mRNA and protein expression levels of CTSS were associated with the expressions of adipogenesis-related genes in skeletal muscle. Overexpression of <i>CTSS</i> promoted adipogenesis in intramuscular preadipocytes, while interference with <i>CTSS</i> inhibited this process. Our findings showed that SNP rs80931414 (A&gt;G), which is a genetic variation in <i>CTSS</i> is related to IMF content and <i>CTSS</i> is a candidate gene for IMF content trait in DLY pig. This study provides the first evidence of the role of <i>CTSS</i> in pig intramuscular preadipocytes and offers insights for the development of breeding strategies aimed at genetically improving IMF content in pork.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"56 2","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-04-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143849313","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":"GTP cyclohydrolase II (gch2) and axanthism in ball pythons: A new vertebrate model for pterin-based pigmentation","authors":"Alan García-Elfring,&nbsp;Heather L. Roffey,&nbsp;Jaren M. Abergas,&nbsp;Andrew P. Hendry,&nbsp;Rowan D. H. Barrett","doi":"10.1111/age.70011","DOIUrl":"https://doi.org/10.1111/age.70011","url":null,"abstract":"<p>Pterin pigments are responsible for many of the bright colors observed across the animal kingdom. However, unlike melanin, the genetics of pterin-based pigmentation has received relatively little attention in animal coloration studies. Here, we investigate a lineage of axanthic ball pythons (<i>Python regius</i>) found in captivity as a model system to study pterin pigmentation in vertebrates. By crowdsourcing shed skin samples from commercial breeders and applying a case–control study design, we used whole-genome pool sequencing (pool-seq) and variant annotation. We identified a premature stop codon in the gene <i>GTP cyclohydrolase II</i> (<i>gch2</i>), which is associated with the axanthic phenotype. GCH2 catalyzes the first rate-limiting step in riboflavin biosynthesis. This study provides the first identification of an axanthism-associated gene in vertebrates and highlights the utility of ball pythons as a model to study pterin-based pigmentation.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"56 2","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143835870","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":"Development of a panel of microhaplotype markers for giant panda","authors":"Wei Xu,&nbsp;Xue Jiang,&nbsp;Minghua Chen,&nbsp;Daxin Xie,&nbsp;Lin Tang,&nbsp;Weide Wang,&nbsp;Xiuyue Zhang,&nbsp;Fujun Shen","doi":"10.1111/age.70008","DOIUrl":"https://doi.org/10.1111/age.70008","url":null,"abstract":"<p>The giant panda is a vulnerable species endemic to China and serves as a flagship species for biodiversity conservation. Accurately assessing population size in small populations has always been the foundation of conservation efforts. Owing to higher dropout rate and instability, the microsatellite marker has always caused the overestimation of the population size. The microhaplotype genetic marker, which is made from several adjacent SNPs, is as stable as the SNP marker and as polymorphic as the microsatellite marker. This study screened a panel of 32 candidate microhaplotype markers with an average polymorphic information content of 0.628 from a whole-genome sequencing dataset of 195 giant pandas. Afterwards, we successfully demonstrated the feasibility and reliability of the microhaplotype markers by genotyping half of them via the Illumina paired-end sequencing, with the markers amplified in four quadruplex PCR reactions, ranging from 142 and 234 bp in length. The cumulative non-exclusion probabilities for the full and half panel of markers are 6.477 × 10⁻²⁷ and 1.444 × 10⁻¹³, respectively. These markers offer a potential tool for individual identification, sex determination, the management and conservation of giant pandas.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"56 2","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143786794","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":"Detecting chromosomal rearrangements in boars using Hi-C","authors":"Frances Burden,&nbsp;Claudia Rathje,&nbsp;Peter Ellis,&nbsp;Justin Holl,&nbsp;Craig R. G. Lewis,&nbsp;Marta Farré","doi":"10.1111/age.70009","DOIUrl":"https://doi.org/10.1111/age.70009","url":null,"abstract":"<p>A chromosomal rearrangement such as a reciprocal translocation (RT) in a breeding boar can produce unbalanced gametes during meiosis, leading to a decreased litter size with detrimental economic implications for breeders. FISH and standard karyotyping are currently used to detect RTs, but a fresh sample is required, limiting the shipping conditions. Here, we investigated Hi-C as an alternative technique to diagnose chromosome rearrangements. We show that Hi-C can be used to detect such RTs from either a fresh or a frozen blood sample and therefore this technique represents an alternative to FISH for RT detection.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"56 2","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/age.70009","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143770128","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":"RNA sequencing analysis reveals key genes and pathways associated with feather pigmentation in mule ducks","authors":"Yifei Wang,&nbsp;Chunhong Zhu,&nbsp;Zhicheng Wang,&nbsp;Weitao Song,&nbsp;Lizhi Lu,&nbsp;Zhiyun Tao,&nbsp;Wenjuan Xu,&nbsp;Shuangjie Zhang,&nbsp;Wei Zhou,&nbsp;Hongxiang Liu,&nbsp;Huifang Li","doi":"10.1111/age.70007","DOIUrl":"https://doi.org/10.1111/age.70007","url":null,"abstract":"<p>Feather color is an important morphological trait of poultry. At present, the reports on the inheritance of plumage color of mule ducks at the molecular level are few, and the regulatory mechanism in white plumage rates of different mule ducks remains unclear. This study aimed to broaden the understanding of the white plumage rates in mule ducks to improve their production value. We used RNA sequencing to analyze and compare the mRNA expression profiles in hair follicle tissues from 10-week-old mule ducks with black and white plumages, thereby revealing the temporal gene expression patterns and pathways associated with plumage color regulation. In total, 1672 annotated differentially expressed genes (DEGs) were identified in black and white plumages from different databases between mule ducks with the 2 plumage colors. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment in hair follicle tissues indicated that the aforementioned DEGs were mainly involved in the melanin signaling pathway. Concurrently, we use weighted gene co-expression network analysis to detect core modules and hub genes associated with melanin biosynthesis in feathers. The green module exhibited the strongest correlation with the phenotypic traits, encompassing a total of 1049 genes. Subsequent Kyoto Encyclopedia of Genes and Genomes enrichment analysis identified 11 genes as pivotal in the melanin biosynthetic pathway, including <i>EDRNB2</i>, <i>TYR</i>, <i>KIT</i>, <i>EDNRB</i>, and <i>MC1R</i>. The differential expression of eight selected DEGs was verified using quantitative reverse transcription–PCR, and the results were consistent with RNA-seq data. This study provides a basis for understanding the differences in plumage color development in mule ducks.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"56 2","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143632920","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":"Two novel SNP variants at ASIP and SNAI2 genes are associated with yellow coat color in rabbits","authors":"Yuan Chen,&nbsp;Hui Wang,&nbsp;Xinxin Ping,&nbsp;Ahamba Ifeanyi Solomon,&nbsp;Zhanjun Ren,&nbsp;Xianggui Dong","doi":"10.1111/age.70006","DOIUrl":"https://doi.org/10.1111/age.70006","url":null,"abstract":"<p>Rabbits display a wide range of coat colors, with yellow being a particular phenotype that aids in exploring the molecular mechanisms of coat pigmentation. The Fujian yellow (FJY) rabbit, as China's only indigenous breed with a yellow coat, serves as a valuable genetic resource. Fujian yellow rabbits have predominantly yellow fur, with a diluted white hue on the distal limbs and tail. However, the genetic mechanism underlying yellow coat color remains unclear. To address this, we conducted selection signature analysis to identify candidate genes and potential casual mutations underlying the yellow phenotype in rabbits. Utilizing whole-genome resequencing, a total of 22 486 177 high-quality SNPs were identified from 30 individuals belonging to three Chinese indigenous rabbit breeds featured with yellow or non-yellow phenotype. The results revealed that the <i>ASIP</i> gene on chromosome 4 and the <i>SNAI2</i> gene on chromosome 3 were under strong selection pressure, both of which play pivotal roles in determining coat color phenotypes. The <i>ASIP</i> gene is involved in melanogenesis across various livestock species, while the <i>SNAI2</i> gene is linked to hypopigmentation in the distal regions such as the limbs and tail. We further identified two SNP variants, g.23870943C&gt;T in the fourth intron of the <i>ASIP</i> gene, which is closely associated with the yellow phenotype, and g.73725380A&gt;G downstream of the <i>SNAI2</i> gene, probably contributing to the white shading in Fujian yellow rabbits’ limb and tail regions. These variants are key determinants in the development of the yellow coat color in rabbits. These findings advance the understanding of coat color pigmentation in domestic animals.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"56 2","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143564517","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 frameshift variant in the SLC6A5 gene is associated with startle disease in a family of Old English Sheepdogs","authors":"Fréderique Boeykens,&nbsp;Michelle Hermans,&nbsp;Laura Adant,&nbsp;Bert De Jonge,&nbsp;Koen Chiers,&nbsp;Kenny Bossens,&nbsp;Bart J. G. Broeckx","doi":"10.1111/age.70003","DOIUrl":"https://doi.org/10.1111/age.70003","url":null,"abstract":"<p>A 2-week-old litter of three Old English Sheepdog puppies presented with episodic generalised muscle hypertonia and cyanosis triggered by touch and noise. Owing to poor response to therapy and progression of symptoms, the puppies were euthanised. Post-mortem histology revealed perineuronal incrustations in the spinal cord, suggestive of ischemia or neuronal necrosis. Clinical symptoms, combined with necropsy and histopathology findings, led to a suspicion of startle disease, prompting a referral to a specialised clinical genetics centre. Whole exome sequencing (WES) of the nuclear family identified a homozygous truncating variant in the <i>SLC6A5</i> gene in affected individuals, with both unaffected parents being heterozygous. Additional population screening found three phenotypically unaffected carriers, indicating that the variant segregates within the Old English Sheepdog breed. This raises concerns about the management of carriers and their breeding contributions if not properly guided by DNA testing. This study addresses a frameshift variant <i>SLC6A5:c.1322del</i> found in Old English Sheepdogs. Next to this, the value of genetic counselling and clinical genetics services in breeding programmes is highlighted to identify carriers and guide informed breeding decisions. Finally, the findings demonstrate the utility of WES in veterinary diagnostics and provide practical insights for breeders, veterinarians and geneticists to improve the health and welfare of Old English Sheepdogs.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"56 2","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143497042","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}