Molecular Genetics and Genomics最新文献_第3页

Role of Php domain and related enzymes in the enzymatic degradation of G-series nerve agents. Php结构域及相关酶在g系列神经毒剂酶降解中的作用。

IF 2.1 3区生物学

Molecular Genetics and Genomics Pub Date : 2025-08-21 DOI: 10.1007/s00438-025-02283-1

Divya Ramamoorthy, Rupa Iyer

引用次数: 0

Genome-wide lipidomic profiling reveals causal lipid species as targets for inguinal hernia risk. 全基因组脂质组学分析揭示了导致腹股沟疝风险的脂质种类。

IF 2.1 3区生物学

Molecular Genetics and Genomics Pub Date : 2025-08-21 DOI: 10.1007/s00438-025-02284-0

Xiaoling Xu, Zemingshan Luo, Xiaojun Xie

{"title":"Genome-wide lipidomic profiling reveals causal lipid species as targets for inguinal hernia risk.","authors":"Xiaoling Xu, Zemingshan Luo, Xiaojun Xie","doi":"10.1007/s00438-025-02284-0","DOIUrl":"https://doi.org/10.1007/s00438-025-02284-0","url":null,"abstract":"Inguinal hernia (IH) is a common condition with a substantial health burden and emerging evidence suggests that lipid metabolism-related indicators may contribute to its risk. However, the exact role of specific lipid types in causing IH is still unclear. This study aims to investigate whether any of 179 distinct lipid species have a causal impact on IH risk using causal inference. We applied a two-sample Mendelian randomization (MR) framework, integrating lipidomic genome-wide association studies (GWAS) data from 7,174 Finnish individuals with IH summary statistics from the UK Biobank (16,749 cases and 439,599 controls). Linkage disequilibrium pruning and genome-wide significance (P < 5E-8) were used to choose genetic instruments. Primary causal estimates were derived with inverse-variance weighted (IVW) method, and further supported by weighted median (WM) and robust adjusted profile score (RAPS). We employed sensitivity tests, like Cochran's Q for heterogeneity, MR-Egger for directional pleiotropy, Radial MR for outlier detection, and leave-one-out analysis to measure the impact of individual variants. Among 179 lipid species, 162 had valid IVs, and 94 met the criteria for causal inference. IVW analysis identified 25 lipid species with nominal significance, 24 of which were supported by WM and RAPS. Sensitivity analyses consistently provided robust evidence supporting a causal relationship between four lipid species and increased IH risk: diacylglycerol (18:1_18:1) (OR = 1.16, P = 0.005), diacylglycerol (18:1_18:2) (OR = 1.12, P = 0.006), phosphatidylinositol (18:0_20:4) (OR = 1.10, P = 1.47E-04), and triacylglycerol (54:6) (OR = 1.21, P = 0.001). Our findings provides genetic molecular evidence that four lipid species are causally linked to an increased IH susceptibility, offering novel insights into lipid-centered interventions for disease prevention and highlighting the importance of metabolic health in hernia pathogenesis.","PeriodicalId":18816,"journal":{"name":"Molecular Genetics and Genomics","volume":"300 1","pages":"78"},"PeriodicalIF":2.1,"publicationDate":"2025-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12370862/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144961759","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}

引用次数: 0

Exploring the genetic footprints of the gotra system in the Koṅkaṇī Sārasvata Brahmins. 探索Koṅkaṇī Sārasvata婆罗门的gotra系统的遗传足迹。

IF 2.1 3区生物学

Molecular Genetics and Genomics Pub Date : 2025-08-12 DOI: 10.1007/s00438-025-02280-4

Jaison Jeevan Sequeira, Swathi Shastri, Pankaj Shrivastava, Ritu Yadav, Bhuvnesh Yadav, Shivkant Sharma, George van Driem, Mohammed S Mustak

{"title":"Exploring the genetic footprints of the gotra system in the Koṅkaṇī Sārasvata Brahmins.","authors":"Jaison Jeevan Sequeira, Swathi Shastri, Pankaj Shrivastava, Ritu Yadav, Bhuvnesh Yadav, Shivkant Sharma, George van Driem, Mohammed S Mustak","doi":"10.1007/s00438-025-02280-4","DOIUrl":"10.1007/s00438-025-02280-4","url":null,"abstract":"The gotra system of exogamy is followed by the Brahmin caste group in India. This system restricts the marriage of individuals who belong to the same gotra. In genetic terms, each gotra forms an exogamous group within a population and thereby maintains a lineage. In Koṅkaṇī Sārasvata Brahmins, the gotras are patrilineal. To understand the genetic footprints of the gotras in this population, we reconstructed the maternal and paternal ancestry of 95 individuals using single nucleotide polymorphism (SNP) markers and Y-chromosomal short tandem repeats (Y-STR). The haplogroup distribution in the gotras showed a significant association with the paternal lineage (p < 0.005) as compared with the maternal lineage. We observed a similar significant association of the gotras with the Y-STR haplotypes. Our findings provide scientific evidence for an actively existing gotra system followed by the caste groups of India. Comparative analysis of 334 Indian Brahmins and over 1300 Eurasian Y-STR profiles showed that all Brahmin groups share a common R1a ancestor with Western Iranian males likely predating the Indo-Iranian split in northern Afghanistan. Whilst North Indian Brahmins shared the lineage with Afghanistan groups, the Koṅkaṇī and southern Brahmins may represent an earlier divergence. The persistence of common gotras throughout India implies the gotra system originated before Brahmin dispersal from north to south. These findings provide genetic evidence for the role of gotra system in shaping Brahmin population structure.","PeriodicalId":18816,"journal":{"name":"Molecular Genetics and Genomics","volume":"300 1","pages":"76"},"PeriodicalIF":2.1,"publicationDate":"2025-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144822038","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}

引用次数: 0

Multi-trait GWAS for growth under contrasting thermal rearing conditions in rainbow trout (Oncorhynchus mykiss). 虹鳟鱼（Oncorhynchus mykiss）在不同热育条件下生长的多性状GWAS。

IF 2.1 3区生物学

Molecular Genetics and Genomics Pub Date : 2025-08-11 DOI: 10.1007/s00438-025-02263-5

Jousepth Gallardo-Hidalgo, David A Tapia, Baltasar F Garcia, Rodrigo Marin-Nahuelpi, Pablo Cáceres, Liane N Bassini, Vito A Mastrochirico-Filho, Carolina Araya, José M Yáñez

{"title":"Multi-trait GWAS for growth under contrasting thermal rearing conditions in rainbow trout (Oncorhynchus mykiss).","authors":"Jousepth Gallardo-Hidalgo, David A Tapia, Baltasar F Garcia, Rodrigo Marin-Nahuelpi, Pablo Cáceres, Liane N Bassini, Vito A Mastrochirico-Filho, Carolina Araya, José M Yáñez","doi":"10.1007/s00438-025-02263-5","DOIUrl":"https://doi.org/10.1007/s00438-025-02263-5","url":null,"abstract":"Thermal variability significantly impacts fish performance, and current breeding objectives may soon be suboptimal due to climate change. Growth is a critical trait for aquaculture profitability. Understanding the genomic differences in growth under varying water temperatures is essential to predict climate change's impact on cold water species production. This study examined a rainbow trout population grown under low (~ 7 °C) and high (~ 22 °C) non-lethal temperatures. The objectives were to: (i) explore the genetic architecture of growth under upper and lower temperature (UT and LT) conditions using multi-trait genome-wide association, and (ii) identify candidate genes and biological processes related to growth in these conditions through a gene-based meta-analysis approach. The results revealed: (i) significant genetic variation for body weight, body length, and average daily gain at both LT and UT conditions, with genomic heritabilities ranging from 0.19 ± 0.06 to 0.32 ± 0.05 and 0.16 ± 0.05 to 0.39 ± 0.08, respectively; (ii) distinct genetic architectures and genes associated with UT and LT growth, with SNP effect correlations from r = 0.06 to 0.22; (iii) shared biological functions for growth at UT and LT, involving cardiovascular function maintenance and cell communication. Cytoskeleton-related functions were predominant in growth at LT, while DNA repair functions were more significant at UT. Notably, sema6ba emerges as a potential candidate gene involved in growth-related traits across contrasting thermal environments in rainbow trout, given its strong association under both low and high temperature conditions.","PeriodicalId":18816,"journal":{"name":"Molecular Genetics and Genomics","volume":"300 1","pages":"75"},"PeriodicalIF":2.1,"publicationDate":"2025-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144817154","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}

引用次数: 0

DNA methylation biomarkers in diabetic kidney disease: insights and implications. DNA甲基化生物标志物在糖尿病肾病：见解和意义。

IF 2.1 3区生物学

Molecular Genetics and Genomics Pub Date : 2025-07-30 DOI: 10.1007/s00438-025-02277-z

Ziyi Feng, Xiaomu Kong, Liang Ma

引用次数: 0

Loss of dcst2 expression in male zebrafish is not associated with muscle hypertrophy. 雄性斑马鱼中dcst2表达的缺失与肌肉肥大无关。

IF 2.1 3区生物学

Molecular Genetics and Genomics Pub Date : 2025-07-30 DOI: 10.1007/s00438-025-02279-x

X Allard-Chamard, E C Rodríguez, B Brais, G A B Armstrong

引用次数: 0

A missense mutation in TCFL5 is associated with male infertility due to oligoasthenoteratozoospermia. TCFL5的错义突变与少弱异卵精子症引起的男性不育有关。

IF 2.3 3区生物学

Molecular Genetics and Genomics Pub Date : 2025-07-25 DOI: 10.1007/s00438-025-02278-y

Kexin Yu, Wenchen Zhang, Yu Wang, Mingfei Xiang, Na Zheng, Jingjing Zhang, Xiaomin Zha, Zongliu Duan, Fengsong Wang, Yunxia Cao, Fuxi Zhu

{"title":"A missense mutation in TCFL5 is associated with male infertility due to oligoasthenoteratozoospermia.","authors":"Kexin Yu, Wenchen Zhang, Yu Wang, Mingfei Xiang, Na Zheng, Jingjing Zhang, Xiaomin Zha, Zongliu Duan, Fengsong Wang, Yunxia Cao, Fuxi Zhu","doi":"10.1007/s00438-025-02278-y","DOIUrl":"https://doi.org/10.1007/s00438-025-02278-y","url":null,"abstract":"Oligoasthenoteratozoospermia (OAT) is a prevalent situation of male infertility partly caused by genetic defects with largely undiscovered. To further unravel the genetic etiology of OAT, we recruited cases for whole-exome sequencing (WES) to screen candidate pathogenic mutations. Here, we identified a heterozygous missense mutation in transcription factor-like 5 (TCFL5) (NM_006602.4: c.1207G > A: p.E403K) from two infertile brothers born into a non-consanguineous family. TCFL5 was previously linked to male infertility since Tcfl5+/- male mice manifested infertile due to OAT, while Tcfl5-/- mice could not be generated. Sperm morphological analysis of these brothers exhibited a similar OAT phenotype to Tcfl5+/- mice. In vitro functional analysis performed to explore the pathogenicity of TCFL5 mutation. Regardless of no significant effect on the expression of mutant TCFL5 detected by western blotting and immunofluorescence, dual-luciferase reporter assay revealed a serious impact on its transcriptional regulatory function. Many crucial genes involved in spermatogenesis, such as DMRT1, DAZL, SYCE1, SPACA1, CNTROB, IFT88, HOOK1 and SPATA6, occurred transcriptional abnormalities after TCFL5 mutated. Our results showed that TCFL5 mutation disrupted the normal transcription of spermatogenesis genes, finally resulting in male infertility raised by OAT. Our work firstly linked TCFL5 mutation to male infertility in human, which provides a new perspective on the genetic underpinnings of OAT and a theoretical basis for clinic genetic counseling and treatment strategies selection.","PeriodicalId":18816,"journal":{"name":"Molecular Genetics and Genomics","volume":"300 1","pages":"72"},"PeriodicalIF":2.3,"publicationDate":"2025-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144708201","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}

引用次数: 0

Unraveling genetic diversity and population structure of pineapple germplasm using genome-wide SNP markers. 利用全基因组SNP标记揭示菠萝种质资源的遗传多样性和群体结构。

IF 2.3 3区生物学

Molecular Genetics and Genomics Pub Date : 2025-07-19 DOI: 10.1007/s00438-025-02275-1

Haomin Lyu, Tracie Matsumoto, Qingyi Yu

{"title":"Unraveling genetic diversity and population structure of pineapple germplasm using genome-wide SNP markers.","authors":"Haomin Lyu, Tracie Matsumoto, Qingyi Yu","doi":"10.1007/s00438-025-02275-1","DOIUrl":"10.1007/s00438-025-02275-1","url":null,"abstract":"Pineapple (Ananas comosus (L.) Merr.) is one of the most important tropical fruits worldwide. It is primarily propagated clonally and exhibits high heterozygosity which can mask deleterious mutations, potentially leading to inbreeding depression and hindering breeding efforts. To address this, we conducted a comprehensive genome-wide analysis of 91 pineapple accessions and identified over 7.9 million high-quality SNPs. We utilized these SNPs to investigate the genetic structure and reproductive patterns of diverse cultivars and related varieties. Population structure analysis revealed a unique genetic makeup of A. comosus var. microstachys accessions and unidirectional gene flow from A. comosus var. microstachys into A. comosus var. comosus, A. comosus var. bracteatus, and A. comosus var. erectifolius. Among the cultivated pineapples, 'Mordilona-related' and 'Smooth Cayenne' cultivars showed unidirectional gene flow from 'Singapore Spanish', 'Queen', and the wild A. comosus var. microstachys. Heterozygosity patterns suggested predominantly asexual reproduction in 'Queen', 'Singapore Spanish', 'Smooth Cayenne', and A. comosus var. microstachys populations, while 'Mordilona-related' and A. comosus var. bracteatus populations might have experienced increased sexual reproduction or population expansion. We developed two SNP panels: one for germplasm identification and the other one for pedigree analysis. These resources will facilitate pineapple germplasm evaluation, diversity analysis, and informed breeding decisions for cultivar improvement.","PeriodicalId":18816,"journal":{"name":"Molecular Genetics and Genomics","volume":"300 1","pages":"71"},"PeriodicalIF":2.3,"publicationDate":"2025-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12276139/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144668020","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}

引用次数: 0

Deciphering gonadal transcriptome reveals circRNA-miRNA-mRNA regulatory network involved in sex differentiation and gametogenesis of Apostichopus japonicus. 对刺参性腺转录组的破译揭示了刺参性别分化和配子发生的circRNA-miRNA-mRNA调控网络。

IF 2.3 3区生物学

Molecular Genetics and Genomics Pub Date : 2025-07-19 DOI: 10.1007/s00438-025-02276-0

Ziming Li, Xinyue Tang, Xinghai Liu, Jing Huo, Ying Guo, Yujia Yang

{"title":"Deciphering gonadal transcriptome reveals circRNA-miRNA-mRNA regulatory network involved in sex differentiation and gametogenesis of Apostichopus japonicus.","authors":"Ziming Li, Xinyue Tang, Xinghai Liu, Jing Huo, Ying Guo, Yujia Yang","doi":"10.1007/s00438-025-02276-0","DOIUrl":"https://doi.org/10.1007/s00438-025-02276-0","url":null,"abstract":"As stable and conserved non-coding RNAs, circular RNAs (circRNAs) play vital roles in gene regulation, particularly in reproductive development. However, their functions in marine invertebrate gonadal differentiation remain largely unexplored. Understanding the molecular mechanisms of sexual differentiation and gonadal development is essential for advancing reproductive biology in marine invertebrates. The sea cucumber Apostichopus japonicus is a vital species in economic aquaculture. Before the breeding season, A. japonicus exhibits minimal sexual dimorphism, significantly impeding breeding efficiency and posing challenges for the development of superior germplasm resources. Investigating the role of circRNAs in mature A. japonicus will enhance our understanding of its specific molecular mechanism during sexual differentiation and gonadal reproduction. In this study, we constructed differential expression profiles of circRNAs. A total of 18,121 circRNAs were identified, distributed across the 23 chromosomes of A. japonicus. 584 circRNAs exhibited significant expression differences, with 296 up-regulated and 288 down-regulated. Through GO enrichment and KEGG pathway analysis of these circRNAs, two pathways related to sexual differentiation were identified: the AMPK signaling pathway and the TGF-β signaling pathway, which may regulate sexual differentiation by influencing sex hormone synthesis. Additionally, several genes, such as smad3, smoc2, and ppp2r1a may play critical regulatory roles in the development and activity of germ cells. Our study elucidates the molecular regulatory roles of circRNAs in the sexual differentiation and gonadal development of A. japonicus. Given its evolutionary position as the closest phylum to chordates, the present study on A. japonicus provides valuable insights into the non-coding RNA resource for marine invertebrates.","PeriodicalId":18816,"journal":{"name":"Molecular Genetics and Genomics","volume":"300 1","pages":"70"},"PeriodicalIF":2.3,"publicationDate":"2025-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144668019","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}

引用次数: 0

Molecular breeding for stress tolerance in sesame. 芝麻抗逆性的分子育种。

IF 2.3 3区生物学

Molecular Genetics and Genomics Pub Date : 2025-07-16 DOI: 10.1007/s00438-025-02274-2

Micheale Yifter Weldemichael, Hailay Mehari Gebremedhn, Steven Runo, Harish Gandhi

{"title":"Molecular breeding for stress tolerance in sesame.","authors":"Micheale Yifter Weldemichael, Hailay Mehari Gebremedhn, Steven Runo, Harish Gandhi","doi":"10.1007/s00438-025-02274-2","DOIUrl":"https://doi.org/10.1007/s00438-025-02274-2","url":null,"abstract":"Sesame (Sesamum indicum L.) is a vital oilseed crop known for its high-quality edible oil, proteins, minerals, and vitamins. It is primarily cultivated in arid and semi-arid regions, where unpredictable drought poses a major constraint to its production. Sesame is a valuable source of healthy vegetable oil, attracting growing interest worldwide. However, its cultivation in dry regions makes it vulnerable to various biotic and abiotic stresses. Sesame is grown for food, pharmaceutical, medicinal, and industrial uses, which is cultivated as a main cash crop by African and Asian smallholder farmers. Despite its importance, sesame production and productivity remain low due to numerous challenges such as; drought, salinity, diseases, insect pests, inherent genetic problems, and poor agronomic and postharvest practices. Fortunately, the crop's extensive genetic diversity offers potential for enhancing stress resilience. Our understanding of sesame molecular responses will be facilitated by ongoing attempts to develop methods for quantifying biotic and abiotic stresses. We review recent advances in the molecular mechanisms underlying sesame's tolerance to biotic and abiotic stresses focusing on stress-related genes and key agronomic traits. Additionally, we review recent advancements in functional genomics and transcriptomics, specifically in deciphering sesame's responses to drought, water-logging, temperature fluctuations, osmotic stress, and salinity as well as biotic stressors. To accelerate the development of stress-resistant sesame varieties, we propose advancing research in genomics-assisted breeding. Approaches such as genome-wide association studies (GWAS) and high-density linkage mapping can help identify key genetic markers associated with stress tolerance. These markers can then be applied in marker-assisted selection to develop resilient cultivars, ensuring stable yields under changing climate conditions.","PeriodicalId":18816,"journal":{"name":"Molecular Genetics and Genomics","volume":"300 1","pages":"69"},"PeriodicalIF":2.3,"publicationDate":"2025-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144642903","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}

引用次数: 0