Mammalian Genome最新文献

Establishing the hybrid rat diversity program: a resource for dissecting complex traits.

IF 2.7 4区生物学

Mammalian Genome Pub Date : 2025-02-05 DOI: 10.1007/s00335-024-10102-y

M R Dwinell, A Takizawa, M Tutaj, L Malloy, R Schilling, A Endsley, W M Demos, J R Smith, S J Wang, J De Pons, A Kundurthi, A M Geurts, A E Kwitek

{"title":"Establishing the hybrid rat diversity program: a resource for dissecting complex traits.","authors":"M R Dwinell, A Takizawa, M Tutaj, L Malloy, R Schilling, A Endsley, W M Demos, J R Smith, S J Wang, J De Pons, A Kundurthi, A M Geurts, A E Kwitek","doi":"10.1007/s00335-024-10102-y","DOIUrl":"https://doi.org/10.1007/s00335-024-10102-y","url":null,"abstract":"Rat models have been a major model for studying complex disease mechanisms, behavioral phenotypes, environmental factors, and for drug development and discovery. Inbred rat strains control for genetic background and allow for repeated, reproducible, cellular and whole animal phenotyping. The Hybrid Rat Diversity Panel (HRDP) was designed to be a powerful panel of inbred rats with genomic, physiological, and behavioral data to serve as a resource for systems genetics. The HRDP consists of 96-98 inbred rat strains aimed to maximize power to detect specific genetic loci associated with complex traits while maximizing the genetic diversity among strains. The panel consists of 32-34 genetically diverse inbred strains and two panels of recombinant inbred panels. To establish the HRDP program, embryo resuscitation and breeding were done to establish colonies for distribution. Whole genome sequencing was performed to achieve 30X coverage. Genomic, phenotype, and strain information is available through the Hybrid Rat Diversity Panel Portal at the Rat Genome Database ( http://rgd.mcw.edu ).","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":" ","pages":""},"PeriodicalIF":2.7,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143189806","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Deciphering the molecular drivers for cashmere/pashmina fiber production in goats: a comprehensive review.

IF 2.7 4区生物学

Mammalian Genome Pub Date : 2025-02-04 DOI: 10.1007/s00335-025-10109-z

Mahanthi Vasu, Sonika Ahlawat, Reena Arora, Rekha Sharma

{"title":"Deciphering the molecular drivers for cashmere/pashmina fiber production in goats: a comprehensive review.","authors":"Mahanthi Vasu, Sonika Ahlawat, Reena Arora, Rekha Sharma","doi":"10.1007/s00335-025-10109-z","DOIUrl":"https://doi.org/10.1007/s00335-025-10109-z","url":null,"abstract":"Cashmere, also known as pashmina, is derived from the secondary hair follicles of Cashmere/Changthangi goats. Renowned as the world's most luxurious natural fiber, it holds significant economic value in the textile industry. This comprehensive review enhances our understanding of the complex biological processes governing cashmere/pashmina fiber development and quality, enabling advancements in selective breeding and fiber enhancement strategies. The review specifically examines the molecular determinants influencing fiber development, with an emphasis on keratins (KRTs) and keratin-associated proteins (KRTAPs). It also explores the roles of key molecular pathways, including Wnt, Notch, BMP, NF-kappa B, VEGF, cAMP, PI3K-Akt, ECM, cell adhesion, Hedgehog, MAPK, Ras, JAK-STAT, TGF-β, mTOR, melanogenesis, FoxO, Hippo, and Rap1 signaling. Understanding these intricate molecular cascades provides valuable insights into the mechanisms orchestrating hair follicle growth, further advancing the biology of this coveted natural fiber. Expanding multi-omics approaches will enhance breeding precision and deepen our understanding of molecular pathways influencing cashmere production. Future research should address critical gaps, such as the impact of environmental factors, epigenetic modifications, and functional studies of genetic variants. Collaboration among breeders, researchers, and policymakers is essential for translating genomic advancements into practical applications. Such efforts can promote sustainable practices, conserve biodiversity, and ensure the long-term viability of high-quality cashmere production. Aligning genetic insights with conservation strategies will support the sustainable growth of the cashmere industry while preserving its economic and ecological value.","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":" ","pages":""},"PeriodicalIF":2.7,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143189777","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genome-wide study for signatures of selection identifies genomic regions and candidate genes associated with milk traits in sheep.

IF 2.7 4区生物学

Mammalian Genome Pub Date : 2025-02-04 DOI: 10.1007/s00335-025-10107-1

Fatemeh Ebrahimi, Mohsen Gholizadeh, Hamid Sahebalam

{"title":"Genome-wide study for signatures of selection identifies genomic regions and candidate genes associated with milk traits in sheep.","authors":"Fatemeh Ebrahimi, Mohsen Gholizadeh, Hamid Sahebalam","doi":"10.1007/s00335-025-10107-1","DOIUrl":"https://doi.org/10.1007/s00335-025-10107-1","url":null,"abstract":"Milk production traits in sheep are influenced by complex genetic factors, and understanding these traits requires the identification of candidate genes under selection. This study employed two methods, FST and XP-EHH, to identify selection signatures and candidate genes associated with milk production traits in sheep. For this purpose, 9 different breeds from the Sheep HapMap dataset generated by the International Sheep Genomics Consortium (ISGC) based on analysis of the Ovine SNP50 BeadChip were used. The dairy breeds included Brown East Friesian (n = 39), Milk Lacaune (n = 103), Chios (n = 23), Churra (n = 120), and Comisana (n = 24), while the non-dairy breeds included Afshari (n = 37), Moghani (n = 34), Galway (n = 49), and Australian Suffolk (n = 109). Genomic regions in the top 0.1 percentile of FST values revealed 71 genes, while regions with the highest positive XP-EHH values identified 69 genes. Five overlapping genes-DHRS3, TNFRSF1B, AADACL4, ARHGEF11, and LRRC71-were detected by both methods, highlighting their relevance to milk production. Several candidate genes in regions identified from FST, such as PER2, SH3PXD2A, TMEM117, DDX6, PDCD11, CALHM2, and CALHM3, have been previously associated with milk production traits. Notably, CRABP2, PEAR1, PGM1, ALG6, COX15, and OAT were identified in regions with high XP-EHH values in the dairy group. Gene ontology analysis indicated that the identified genes are enriched in pathways related to chemokine receptor activity, gap junction channel activity, and gap junction-mediated intercellular transport, as well as cellular components like the connexin complex. Further studies on these genes may improve understanding of the genetic architecture of milk production traits in sheep.","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":" ","pages":""},"PeriodicalIF":2.7,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143189822","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Commentary: towards a national research infrastructure strategy for preclinical biological models in Australia. 评论：朝着澳大利亚临床前生物学模型的国家研究基础设施战略。

IF 2.7 4区生物学

Mammalian Genome Pub Date : 2025-01-20 DOI: 10.1007/s00335-024-10103-x

James E Hennessy, Sarah Nisbet, Michael S Dobbie

{"title":"Commentary: towards a national research infrastructure strategy for preclinical biological models in Australia.","authors":"James E Hennessy, Sarah Nisbet, Michael S Dobbie","doi":"10.1007/s00335-024-10103-x","DOIUrl":"https://doi.org/10.1007/s00335-024-10103-x","url":null,"abstract":"Research infrastructure is critical for advancing knowledge of health and disease, fostering innovation through world-class, cutting-edge facilities and technical expertise. Phenomics Australia is Australia's national research infrastructure provider responsible for accelerating advances in mammalian functional genomics and precision medicine through the development and delivery of services and expertise in engineered disease model production, phenotyping, and biobanking. These capabilities and resources are enabled by Australia's National Collaborative Research Infrastructure Strategy and primarily support health and medical research for significant healthcare and economic benefits. Priorities identified in the Australian Government's 2021 National Research Infrastructure Roadmap include the development and expansion of capabilities in digital research infrastructure, improved research translation, and enhanced management of biological collections, which are strongly aligned with Phenomics Australia's strategy to develop and enable access to high-quality national genetics resources at scale. Here, we comment on Phenomics Australia's response to these national strategy imperatives and the critical role of preclinical biological models research infrastructure in Australia.","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":" ","pages":""},"PeriodicalIF":2.7,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143008016","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

CTNNB1 syndrome mouse models. CTNNB1综合征小鼠模型。

IF 2.7 4区生物学

Mammalian Genome Pub Date : 2025-01-20 DOI: 10.1007/s00335-025-10105-3

Duško Lainšček, Vida Forstnerič, Špela Miroševič

{"title":"CTNNB1 syndrome mouse models.","authors":"Duško Lainšček, Vida Forstnerič, Špela Miroševič","doi":"10.1007/s00335-025-10105-3","DOIUrl":"https://doi.org/10.1007/s00335-025-10105-3","url":null,"abstract":"CTNNB1 syndrome is a rare neurodevelopmental disorder, affecting children worldwide with a prevalence of 2.6-3.2 per 100,000 births and often misdiagnosed as cerebral palsy. De novo loss-of-function mutations in the Ctnnb1 gene result in dysfunction of the β-catenin protein, disrupting the canonical Wnt signaling pathway, which plays a key role in cell proliferation, differentiation, and tissue homeostasis. Additionally, these mutations impair the formation of cell junctions, adversely affecting tissue architecture. Motor and speech deficits, cognitive impairment, cardiovascular and visual problems are just some of the key symptoms that occur in CTNNB1 syndrome patients. There is currently no effective treatment option available for patients with CTNNB1 syndrome, with support largely focused on the management of symptoms and physiotherapy, yet recently some therapeutic approaches are being developed. Animal testing is still crucial in the process of new drug development, and mouse models are particularly important. These models provide researchers with new understanding of the disease mechanisms and are invaluable for testing the efficacy and safety of potential treatments. The development of various mouse models with β-catenin loss- and gain-of-function mutations successfully replicates key features of intellectual disability, autism-like behaviors, motor deficits, and more. These models provide a valuable platform for studying disease mechanisms and offer a powerful tool for testing the therapeutic potential and effectiveness of new drug candidates, paving the way for future clinical trials.","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":" ","pages":""},"PeriodicalIF":2.7,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143008017","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Identification of a critical interval for type 2 diabetes QTL on chromosome 4 in DDD-A^y mice. DDD-Ay小鼠4号染色体上2型糖尿病QTL关键区间的鉴定

IF 2.7 4区生物学

Mammalian Genome Pub Date : 2025-01-20 DOI: 10.1007/s00335-025-10106-2

Jun-Ichi Suto, Misaki Kojima

{"title":"Identification of a critical interval for type 2 diabetes QTL on chromosome 4 in DDD-Ay mice.","authors":"Jun-Ichi Suto, Misaki Kojima","doi":"10.1007/s00335-025-10106-2","DOIUrl":"https://doi.org/10.1007/s00335-025-10106-2","url":null,"abstract":"Type 2 diabetes mellitus (T2D) in male KK-Ay and B6-Ay mice is typically associated with hyperinsulinemia, whereas male DDD-Ay mice exhibit a marked decrease in circulating insulin levels due to the loss of pancreatic islet β-cells. T2D in male DDD-Ay mice is linked to Nidd/DDD, a significant quantitative trait locus (QTL) mapped with a 95% confidence interval (CI) between 112.44 and 151.47 Mbp on chromosome 4. Several T2D QTLs involving Nidd/SJL and Nidd/DBA have been identified on this chromosome; however, their allelic relationships remain unclear. In this study, two sets of male F2-Ay mice produced by crossing C57BL/6J and DDD-Ay mice, and C3H/HeJ and DDD-Ay mice, were used to narrow the 95% CI of the Nidd/DDD to a 9.4 Mbp interval between 114.65 and 125.05 Mbp. Candidate genes underlying Nidd/DDD were identified, assuming that the causative variant is a nonsynonymous single nucleotide variant (nsSNV). The analysis identified 48 potential candidate nsSNVs unique to DDD-Ay mice compared to those in KK, B6, C3H, and DBA mice. Among these nsSNVs, 18 were identified in olfactory receptor genes, which have recently been implicated in the pathogenesis of T2D. The 9.4 Mbp region also contained Zfp69, a potential causative gene for Nidd/SJL, suggesting that Nidd/DDD could be allelic to Nidd/SJL but not to Nidd/DBA. In summary, the findings of this study provide insights into the allelic relationships between T2D QTLs on murine chromosome 4 and their underlying causative genetic variations.","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":" ","pages":""},"PeriodicalIF":2.7,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143008020","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Identification of cis-sQTL demonstrates genetic associations and functional implications of inflammatory processes in Nelore cattle muscle tissue. 顺式- sqtl的鉴定证明了内洛雷牛肌肉组织炎症过程的遗传关联和功能意义。

IF 2.7 4区生物学

Mammalian Genome Pub Date : 2025-01-18 DOI: 10.1007/s00335-024-10100-0

Thaís Cristina Ferreira Dos Santos, Evandro Neves Silva, Gabriela Bonfá Frezarim, Bruna Maria Salatta, Fernando Baldi, Larissa Fernanda Simielli Fonseca, Lucia Galvão De Albuquerque, Maria Malane Magalhães Muniz, Danielly Beraldo Dos Santos Silva

{"title":"Identification of cis-sQTL demonstrates genetic associations and functional implications of inflammatory processes in Nelore cattle muscle tissue.","authors":"Thaís Cristina Ferreira Dos Santos, Evandro Neves Silva, Gabriela Bonfá Frezarim, Bruna Maria Salatta, Fernando Baldi, Larissa Fernanda Simielli Fonseca, Lucia Galvão De Albuquerque, Maria Malane Magalhães Muniz, Danielly Beraldo Dos Santos Silva","doi":"10.1007/s00335-024-10100-0","DOIUrl":"https://doi.org/10.1007/s00335-024-10100-0","url":null,"abstract":"This study aimed to identify splicing quantitative trait loci (cis-sQTL) in Nelore cattle muscle tissue and explore the involvement of spliced genes (sGenes) in immune system-related biological processes. Genotypic data from 80 intact male Nelore cattle were obtained using SNP-Chip technology, while RNA-Seq analysis was performed to measure gene expression levels, enabling the integration of genomic and transcriptomic datasets. The normalized expression levels of spliced transcripts were associated with single nucleotide polymorphisms (SNPs) through an analysis of variance using an additive linear model with the MatrixEQTL package. A permutation analysis then assessed the significance of the best SNPs for each spliced transcript. Functional enrichment analysis was performed on the sGenes to investigate their roles in the immune system. In total, 3,187 variants were linked to 3,202 spliced transcripts, with 83 sGenes involved in immune system processes. Of these, 31 sGenes were enriched for five transcription factors. Most cis-sQTL effects were found in intronic regions, with 27 sQTL variants associated with disease susceptibility and resistance in cattle. Key sGenes identified, such as GSDMA, NLRP6, CASP6, GZMA, CASP4, CASP1, TREM2, NLRP1, and NAIP, were related to inflammasome formation and pyroptosis. Additionally, genes like PIDD1, OPTN, NFKBIB, STAT1, TNIP3, and TREM2 were involved in regulating the NF-kB pathway. These findings lay the groundwork for breeding disease-resistant cattle and enhance our understanding of genetic mechanisms in immune responses.","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":" ","pages":""},"PeriodicalIF":2.7,"publicationDate":"2025-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143008021","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

IMPC impact on preclinical mouse models. IMPC对临床前小鼠模型的影响。

IF 2.7 4区生物学

Mammalian Genome Pub Date : 2025-01-16 DOI: 10.1007/s00335-025-10104-4

Sabine M Hölter, Pilar Cacheiro, Damian Smedley, K C Kent Lloyd

引用次数: 0

Genome engineering with Cas9 and AAV repair templates, successes and pitfalls. 基因组工程与Cas9和AAV修复模板，成功与缺陷。

IF 2.7 4区生物学

Mammalian Genome Pub Date : 2025-01-13 DOI: 10.1007/s00335-024-10099-4

M C Birling, Y Hérault, G Pavlovic

引用次数: 0

Molecular diversity and phylogenetic analysis of ten sheep breeds from Khyber Pakhtunkhwa, Pakistan, based on mitochondrial D-loop sequences. 基于线粒体 D-loop 序列的巴基斯坦开伯尔巴图克瓦省 10 个绵羊品种的分子多样性和系统发育分析。

IF 2.7 4区生物学

Mammalian Genome Pub Date : 2024-12-30 DOI: 10.1007/s00335-024-10093-w

Shabir Ahmed, Muhammad Shahid Nadeem, Anna M Johansson, Elisabeth Jonas, Khushi Muhammad, Sardar Azhar Mehmood

{"title":"Molecular diversity and phylogenetic analysis of ten sheep breeds from Khyber Pakhtunkhwa, Pakistan, based on mitochondrial D-loop sequences.","authors":"Shabir Ahmed, Muhammad Shahid Nadeem, Anna M Johansson, Elisabeth Jonas, Khushi Muhammad, Sardar Azhar Mehmood","doi":"10.1007/s00335-024-10093-w","DOIUrl":"https://doi.org/10.1007/s00335-024-10093-w","url":null,"abstract":"Livestock farming has a key role in many rural communities both economically and culturally. It plays an important role in overcoming the deficiencies of meat, milk, wool and various by-products. Pakistan has a large number of livestock, well-adapted to local conditions. and has some of the best tropical dairy breeds. Native sheep breeds stand a vital asset to the country's livestock sector because of their adaptability and unique genetic traits. However, knowledge of the genetic diversity of these sheep breeds remains limited. This study aims to investigate the genetic diversity of 10 local sheep breeds from Khyber Pakhtunkhwa by analyzing the mitochondrial D-loop from 159 individual samples of females. The sequenced data from the mtDNA D-loop showed 106 different haplotypes, with a haplotype diversity of 0.9854 ± 0.0041. Analysis of the mitochondrial D-loop revealed three distinct haplogroups (HapA, HapB, and HapC). Out of the 159 sequences, 125 (77.99%) grouped with HapA, 30 (18.87%) with HapB, and 5 (3.14%) with HapC. While HapA and HapB are commonly found in sheep breeds worldwide, the identification of 5 sequences belonging to HapC was unexpected. This haplogroup was seen in four sheep breeds: Afghani, Australian, Gauder and Waziri. Most interestingly, the two Pakistani-origin breeds, the Waziri sheep breed, from South of Waziristan and the Gauder, a crossbreed, have been identified with HapC haplogroup. This indicates that the sheep breeds of Khyber Pakhtunkhwa belong to three distinct phylogenetic lineages, suggesting a probable gene flow from the southwest to the northeast regions of the province.","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":" ","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142910002","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0