Animal genetics最新文献

{"title":"Animal genetics 100 years ago","authors":"Frank W. Nicholas","doi":"10.1111/age.70017","DOIUrl":"https://doi.org/10.1111/age.70017","url":null,"abstract":"<p>One hundred years ago, the first book with the phrase “Animal Genetics” in its title was published. It was written by F.A.E. Crew, then Lecturer in Genetics and foundation Director of the Department of Research in Animal Breeding at the University of Edinburgh. The 352 pages of text provide a most interesting summary of the knowledge of animal genetics at that time. It is impressive to see the extent to which the understanding of genetics had developed in just a couple of decades since the rediscovery of Mendelism. There was, for example, recognition that genes are borne on chromosomes; that XX/XY sex determination provides a very satisfactory explanation for most of the relevant evidence; that sex-linked inheritance has a practical application; that variation in quantitative traits is determined by the combined action of many genes and many non-genetic factors; that inbreeding results in substantial decreases in fecundity and fertility due to homozygosity for undesirable alleles; that crossing between lines or breeds gives rise to hybrid vigour (heterosis); and that many disorders are inherited in a Mendelian fashion, and hence can be controlled by informed breeding. There is, however, no mention of Fisher's 1918 paper nor of Wright's recently published inbreeding coefficient and coefficient of relationship. Crew's book inspired the next generation of geneticists, such as Fred Hutt, who travelled from Canada to Edinburgh to do a PhD with Crew, and who later published his own very influential book with the same title, which was dedicated to Crew.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"56 3","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/age.70017","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144074285","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":"Analysis of genetic diversity and selection signatures on the Zhashi Brown goat through whole genome sequencing data","authors":"Shuang Li,&nbsp;Hong Lei,&nbsp;Zulfiqar Ahmed,&nbsp;Hongfeng Duan,&nbsp;Jianbo Li,&nbsp;Haobang Li,&nbsp;Chuzhao Lei,&nbsp;Baizhong Zhang,&nbsp;Kangle Yi","doi":"10.1111/age.70016","DOIUrl":"https://doi.org/10.1111/age.70016","url":null,"abstract":"<p>The Zhashi Brown goat is native to Hengyang Municipality in Hunan Province in southern China and boasts a rich history. The goats exhibit exceptional traits, including heat and insect resistance, strong reproductive capabilities and superior meat production. Despite these merits, the currently limited population requires immediate conservation endeavors. In this study, we conducted whole-genome resequencing on 21 Zhashi Brown goats. Additionally, we performed a joint analysis using published whole-genome data from 119 goats, including Chengdu Brown goat, Matou goat, Wuxue goat, Xiangdong Black goat, Qaidam Cashmere goat, Ujumqin Cashmere goat and Shanbei Cashmere goat. The results revealed that the Zhashi Brown goat is genetically more pure than other Southern Chinese goat breeds. Furthermore, the genetic diversity (nucleotide diversity, linkage disequilibrium, runs of homozygosity and inbreeding coefficient) of the Zhashi Brown goat's genome is at a low level among the eight breeds, indicating the need for further conservation. Employing analytical methodologies such as composite likelihood ratio, nucleotide diversity, integrated haplotype score, the fixation index and cross-population extended haplotype homozygosity, we systematically scanned selective signals within the genomic landscape of Zhashi Brown goat. The outcomes underscore strong selection signals associated with genes implicated in immune response, heat tolerance, reproductive performance and meat quality. These findings make a significant contribution to our understanding of the genetics framework associated with adaptive traits in Zhashi Brown goat. Furthermore, this study explores the genetic diversity of the Zhashi Brown goat, which may contribute to the theoretical framework for conserving its genetic resources, while the identified trait-associated variations could inform future strategies to optimize selective breeding programs.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"56 3","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143944633","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":"Genome-wide analysis of genetic diversity and selection signatures in Fuzhou cattle","authors":"Nan Wang,&nbsp;Yushan Li,&nbsp;Xinyi Li,&nbsp;Hao Li,&nbsp;Chenqi Bian,&nbsp;Xinyu Chen,&nbsp;Halima Jafari,&nbsp;Ningbo Chen,&nbsp;Chuzhao Lei","doi":"10.1111/age.70015","DOIUrl":"https://doi.org/10.1111/age.70015","url":null,"abstract":"<p>The Fuzhou cattle breed, native to northeast China, is widely recognized for its adaptability, disease resistance, and docility. Despite being known for these qualities, its population has declined recently, and there is a significant lack of genomic studies on this species. We sequenced 21 samples from a primary breeding farm to determine the genetic structure, diversity, and selection signature to address this. Additionally, we combined 100 published genomic datasets from diverse geographical regions to characterize the genomic variation of Fuzhou cattle. There were 53 752 978 bi-allelic SNPs retained for downstream analysis. In population structure analysis, Fuzhou cattle show a predominantly East Asian taurine ancestry, with strong genetic affinities to Hanwoo and Yanbian cattle. Despite high nucleotide diversity within the Bos taurine lineage, genetic diversity analysis also revealed significant levels of inbreeding in Fuzhou cattle populations, indicating the need for conservation. Utilizing various methods such as <i>θπ</i>, iHS, <i>F</i>_ST, <i>π</i>-ratio, and XP-EHH, we identified genes associated with traits like growth, meat quality, energy metabolism, and immunity. Several genes related to cold adaptation were identified, including <i>PLIN5</i>, <i>PLB1</i>, and <i>CPT2</i>. These findings provide a basis for conservation strategies to safeguard the genetic resources of Fuzhou cattle.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"56 3","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143908923","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":"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}