BMC Genomics最新文献

{"title":"Identifying cross-tissue molecular targets of lung function by multi-omics integration analysis from DNA methylation and gene expression of diverse human tissues.","authors":"Shisheng Peng, Jinlong Fang, Weiliang Mo, Guodong Hu, Senquan Wu","doi":"10.1186/s12864-025-11476-2","DOIUrl":"10.1186/s12864-025-11476-2","url":null,"abstract":"<p><strong>Background: </strong>Previous studies have reported several genetic loci associated with lung function. However, the mediating mechanism between these genetic loci and lung function phenotype is rarely explored. In this research, we used a cross-tissue multi-omics post-GWAS analysis to explain the associations between DNA methylation, gene expression, and lung function.</p><p><strong>Methods: </strong>We conducted integration analyses of lung function traits using genome-wide association study (GWAS) summary data alongside expression quantitative trait loci (eQTLs) and DNA methylation quantitative trait loci (mQTLs) derived from whole blood, utilizing multi-omics SMR and Bayesian colocalization analysis. Considering the genetic differences of tissues, we replicated the shared causal signals of eQTLs and lung function in 48 diverse tissues and the shared causal signals of mQTLs and lung function in 8 diverse tissues. Multi-trait colocalization analyses were utilized to identify the causal signals between gene expression in blood, blood cell traits, and lung function, as well as between cross-tissue gene expression in diverse tissues and lung function.</p><p><strong>Results: </strong>Eight genes from blood tissue were prioritized as FEV1 causal genes using multi-omics SMR analysis and COLOC colocalization analysis: EML3, UBXN2A, ROM1, ZBTB38, RASGRP3, FAIM, PABPC4, and SNIP1. Equally, five genes (CD46, EML3, UBXN2A, ZBTB38, and LMCD1) were prioritized as FVC causal genes and one gene (LMCD1) was prioritized as FEV1/FVC causal genes. The causal signals between 8 genes (EML3, ROM1, UBXN2A, ZBTB38, RASGRP3, FAIM, PABPC4, and CD46) and lung function were successfully replicated in diverse tissues. More importantly, MOLCO colocalization analysis showed that 3 genes (CD46, LMCD1, and ZBTB38) expression in blood, blood cell traits, and lung function traits shared the same causal signals. Finally, through cross-tissue colocalization analysis of multiple traits, we found that the heart-lung axis EML3 expressions and lung function mediate the same causal signal.</p><p><strong>Conclusion: </strong>This study identified potential cross-tissue molecular targets associated with lung function traits from DNA methylation and gene expression of diverse tissues and explored the probable regulation mechanism of these molecular targets. This provides multi-omics and cross-tissue evidence for the molecular regulation mechanism of lung function and may provide new insight into the influence of crosstalk between organs and tissues on lung function.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"289"},"PeriodicalIF":3.5,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11931835/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143699484","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative mitogenomic analysis of Chinese cavefish Triplophysa (Cypriniformes: Nemacheilidae): novel gene tandem duplication and evolutionary implications.","authors":"Shuang Song, Jianhan Cao, Hongmei Xiang, Zhixiao Liu, Wansheng Jiang","doi":"10.1186/s12864-025-11486-0","DOIUrl":"10.1186/s12864-025-11486-0","url":null,"abstract":"<p><strong>Background: </strong>Cavefish exhibit significant morphological changes that result in trade-offs in metabolic requirements and energy utilization in perpetual darkness. As cellular \"powerhouses\", mitochondria play crucial roles in energy metabolism, suggesting that mitochondrial genes have likely experienced selective pressures during cavefish evolution.</p><p><strong>Results: </strong>This study presents the first assembly of the complete mitogenome of Triplophysa yangi, a typical cavefish species in China. The mitogenome is 17,068 bp long, marking the longest recorded for the genus Triplophysa, and includes 13 protein-coding genes (PCGs), 2 rRNAs, 25 tRNAs, and a noncoding control region. An ~ 500 bp insertion between ND2 and WANCY regions was observed, comprising a large intact tandem repeat unit (A'-N'-OL'-C') flanked by two unannotated sequences (U1/U2). The evolutionary origin of this repeat unit may involve either in situ duplication events with subsequent functional divergence-where neofunctionalization, subfunctionalization, or pseudogenization drove differential mutation rates between paralogs-or alternatively, horizontal acquisition from exogenous genetic material that became functionally integrated into the ancestral T. yangi mitogenome through co-option mechanisms. Phylogenetic analyses revealed two major clades within Triplophysa-epigean and hypogean lineages-consistent with previous classifications, while cave-restricted species exhibited signs of parallel evolution within the hypogean lineage. Selective pressure analysis indicated that the hypogean lineage (cave-dwelling groups, II & III) have a significantly increased ratio of nonsynonymous to synonymous substitution rates (ω) compared to the epigean lineage (surface-dwelling group, I), suggesting a combination of adaptive selection and relaxed functional constraints in cave-dwelling species.</p><p><strong>Conclusions: </strong>The duplication of tRNAs in T. yangi and the potential positive selection sites identified in Triplophysa cavefish further indicated adaptive evolution in mitochondrial PCGs in response to extreme subterranean conditions.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"293"},"PeriodicalIF":3.5,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11934697/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143699461","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Application of genomic tools to study and potentially improve the upper thermal tolerance of farmed Atlantic salmon (Salmo salar).","authors":"Eric H Ignatz, Melissa S Allen, Jennifer R Hall, Rebeccah M Sandrelli, Mark D Fast, Guy M L Perry, Matthew L Rise, A Kurt Gamperl","doi":"10.1186/s12864-025-11482-4","DOIUrl":"10.1186/s12864-025-11482-4","url":null,"abstract":"<p><strong>Background: </strong>The Atlantic salmon (Salmo salar) aquaculture industry must mitigate the impacts of rising ocean temperatures and the increased prevalence/severity of marine heat waves. Therefore, we investigated the genetic architecture and gene expression (transcriptomics) responsible for determining a salmon's upper thermal tolerance.</p><p><strong>Results: </strong>A genome-wide association study (GWAS) was conducted using fin clips of salmon from a previous incremental thermal maximum (IT_Max) challenge (n = 251) and the North American 50 K SNP chip. IT_Max was a highly polygenic trait with low/moderate heritability (mean SNP-based h² = 0.20 and pedigree-based h² = 0.25). Using data from the same fish, a separate GWAS assessed thermal-unit growth coefficient (TGC). Five significant SNPs were detected on chromosomes three and five, and high heritability estimates were calculated for TGC measured as fish grew from 12 to 20 °C (mean SNP-based h² = 0.62 and pedigree-based h² = 0.64). RNA-seq analyses of liver samples (n = 5-6 family^-1 temperature^-1) collected from the four most and four least tolerant families at 10 and 20 °C were also used to provide insights into potential mechanisms modulating this species' thermal tolerance. Between the top and bottom families, 347 and 175 differentially expressed transcripts (FDR-adjusted p < 0.01; fold-change ≥|2.0|) were identified at 10 and 20 °C, respectively. GO term enrichment analysis revealed unique responses to elevated temperature between family rankings (e.g., 'blood coagulation', 'sterol metabolic process' and 'synaptic growth at neuromuscular junction'). qPCR analyses further confirmed differences pertaining to cholesterol metabolism (lpl), inflammation (epx, elf3, ccl20), apoptosis (htra1b, htra2, anxa5b), angiogenesis (angl4, pdgfa), nervous system processes (insyn2a, kcnj11l) and heat stress (serpinh1b-1, serpinh1b-2). Three differentially expressed transcripts (i.e., ppp1r9a, gal3st1a, f5) were located in close proximity (± 120 kbp) to near-significant SNPs from the GWAS. Interestingly, ppp1r9a and gal3st1a have putative neurological functions, while f5 regulates blood coagulation.</p><p><strong>Conclusions: </strong>These analyses provide several putative biomarkers of upper thermal tolerance in salmon that could prove valuable in helping the industry develop more temperature-tolerant fish. Further, our study supports previous reports that IT_Max has low/moderate heritability in this species, and suggests that TGC at elevated temperatures is highly heritable.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"294"},"PeriodicalIF":3.5,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11934803/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143699296","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic insights into the genetic diversity and genetic basis of body height in endangered Chinese Ningqiang ponies.","authors":"Jiale Han, Hanrui Shao, Minhao Sun, Feng Gao, Qiaoyan Hu, Ge Yang, Halima Jafari, Na Li, Ruihua Dang","doi":"10.1186/s12864-025-11484-2","DOIUrl":"10.1186/s12864-025-11484-2","url":null,"abstract":"<p><strong>Background: </strong>Genetic diversity in livestock and poultry is critical for adapting production systems to future challenges. However, inadequate management practices, particularly in developing countries, have led to the extinction or near extinction of several species. Understanding the genetic composition and historical background of local breeds is essential for their effective conservation and sustainable use. This study compared the genomes of 30 newly sequenced Ningqiang ponies with those of 56 other ponies and 104 horses to investigate genetic diversity, genetic differentiation, and the genetic basis of body height differences.</p><p><strong>Result: </strong>Population structure and genetic diversity analyses revealed that Ningqiang ponies belong to southwestern Chinese ponies. They exhibit a moderate level of inbreeding compared to other pony and horse breeds. Mitochondrial DNA analysis indicated that Ningqiang and Debao ponies share the dominant haplogroups A and C, suggesting a likely common maternal origin. Our study identified low genetic differentiation and detectable gene flow between Ningqiang ponies and Datong horses. The study also indicated the effective population size of Ningqiang ponies showed a downward trend. These findings potentially reflect the historical formation of Ningqiang ponies and population size changes. A selection signal scan (CLR and θπ) within Ningqiang ponies detected several key genes associated with bone development (ANKRD11, OSGIN2, JUNB, and RPL13) and immune response (RIPK2). The combination of genome-wide association analysis and selective signature analysis (F_ST) revealed significant single nucleotide polymorphisms and selective genes associated with body height, with the most prominent finding being the TBX3 gene on equine chromosome (ECA) 8. Additionally, TBX5, ASAP1, CDK12, CA10, and CSMD1 were identified as important candidate genes for body height differences between ponies and horses.</p><p><strong>Conclusion: </strong>The results of this study elucidate the genetic diversity, genetic differentiation, and effective population size of Ningqiang ponies compared to other ponies and horses, further deepen the understanding of their small stature, and provide valuable insights into the conservation and breeding of local horse breeds in China.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"292"},"PeriodicalIF":3.5,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11934595/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143699449","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification and functional validation of a novel FBN1 variant in a Marfan syndrome family using a zebrafish model.","authors":"Shitong Huang, Jiansong Chen, Qiuyu Wang, Ruyue Zhang, Jian Zhuang, Ruiyuan Huang, Changjiang Yu, Miaoxian Fang, Haishan Zhao, Liming Lei","doi":"10.1186/s12864-025-11471-7","DOIUrl":"10.1186/s12864-025-11471-7","url":null,"abstract":"<p><strong>Background: </strong>Marfan syndrome (MFS) is an inherited autosomal dominant disorder that affects connective tissue with an incidence of about 1 in 5,000 to 10,000 people. 90% of MFS is caused by mutations in the fibrillin-1 (FBN1) gene. We recruited a family with MFS phenotype in South China and identified a novel variant. This study investigated whether this genetic variant is pathogenic and the potential pathway related to lipid metabolism in MFS.</p><p><strong>Methods: </strong>A three-generation consanguineous family was recruited for this study. Whole exome sequencing (WES) was utilized on family members. The 3D structure of the protein was predicted using AlphaFold. CRISPR/Cas9 was applied to generate a similar fbn1 nonsense mutation (fbn1^+/-) in zebrafish. RNA-seq analysis on zebrafish was performed to identify potential pathways related to MFS pathogenesis.</p><p><strong>Results: </strong>Our study identified a novel variant [NM_000138.5; c.7764 C > G: p.(Y2588*)] in FBN1 gene from the family and identified the same site mutation among the proband along with her son and daughter. Structural modeling showed the p.Y2588* mutation resulted from a truncated protein. Compared to wild-type zebrafish, the F2 generation fbn1^+/- zebrafish exhibited MFS phenotype. RNA-seq analysis indicated that many genes related to leptin are up-regulating, which could affect bone development and adipose homeostasis.</p><p><strong>Conclusion: </strong>A novel variant was identified in FBN1 gene. In a zebrafish model, we found functional evidence supporting the pathogenicity of the detected nonsense mutation. Our research proposes a possible mechanism underlying the relationship between lipid metabolism and MFS. These findings can help improve the clinical diagnosis and treatment of MFS.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"288"},"PeriodicalIF":3.5,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11931800/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143699453","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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-wide identification and analysis of GH1-containing H1 histones among poplar species.","authors":"Ping Li, Jing Wang, Qimin Zhang, Anmin Yu, Rui Sun, Aizhong Liu","doi":"10.1186/s12864-025-11456-6","DOIUrl":"10.1186/s12864-025-11456-6","url":null,"abstract":"<p><p>Histone H1s are basic nuclear proteins, which played key role in the binding of DNA and nucleosome, eventually the stability of eukaryotic chromatin. In most species, H1s possess an evolutionarily conserved nucleosome-DNA binding globular domain (GH1), which is conserved between species, especially in mammals. However, there is limited information on the phylogeny, structure and function of H1s in poplar. In the present research, 21 GH1-containing proteins found in Populus trichocarpa were classified into three subgroups (H1s, Myb (SANK) GH1 and AT-hook GH1) based on their domains. The Populus H1 proteins contained lysine-rich N-, C-terminal tails and a conserved GH1 domain, particularly the characteristic amino acids in the helix and strand structures of the five H1 subtypes. The phylogenetic and structure diversity analysis of GH1 proteins across different Populus species and model plants revealed three conserved subgroups with characteristic amino acids. The variation in the number of members across the five subtypes was consistent with the evolutionary relationships among Populus species. The conserved characteristic amino acids among same Populus subtype can be served as markers for subtype identification. Furthermore, the abundance analysis of H1s in Populus indicated their unique functions in young tissues and stages, which may be related to DNA methylation. The consistent expression pattern of H1 across Populus species was in accordance with collinearity pairs. Present analyses provided valuable information on the diversity and evolution of H1s in Populus, advocating further research of H1s in plants.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"287"},"PeriodicalIF":3.5,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11931866/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143699479","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multi-tool copy number detection highlights common body size-associated variants in miniature pig breeds from different geographical regions.","authors":"Jan Berghöfer, Nadia Khaveh, Stefan Mundlos, Julia Metzger","doi":"10.1186/s12864-025-11446-8","DOIUrl":"10.1186/s12864-025-11446-8","url":null,"abstract":"<p><strong>Background: </strong>Copy number variations (CNVs) represent a common and highly specific type of variation in the genome, potentially influencing genetic diversity and mammalian phenotypic development. Structural variants, such as deletions, duplications, and insertions, have frequently been highlighted as key factors influencing traits in high-production pigs. However, comprehensive CNV analyses in miniature pig breeds are limited despite their value in biomedical research.</p><p><strong>Results: </strong>This study performed whole-genome sequencing in 36 miniature pigs from nine breeds from America, Asia and Oceania, and Europe. By employing a multi-tool approach (CNVpytor, Delly, GATK gCNV, Smoove), the accuracy of CNV identification was improved. In total, 34 homozygous CNVs overlapped with exonic regions in all samples, suggesting a role in expressing specific phenotypes such as uniform growth patterns, fertility, or metabolic function. In addition, 386 copy number variation regions (CNVRs) shared by all breeds were detected, covering 33.6 Mb (1.48% of the autosomal genome). Further, 132 exclusive CNVRs were identified for American breeds, 47 for Asian and Oceanian breeds, and 114 for European breeds. Functional enrichment analysis revealed genes within the common CNVRs involved in body height determination and other growth-related parameters. Exclusive CNVRs were located in the region of genes enriched for lipid metabolism in American minipigs, reproductive traits in Asian and Oceanian breeds, and cardiovascular features and body height in European breeds. In the selected groups, quantitative trait loci associated with body size, meat quality, reproduction, and disease susceptibility were highlighted.</p><p><strong>Conclusion: </strong>This investigation of the CNV landscape of minipigs underlines the impact of selective breeding on structural variants and its role in the development of specific breed phenotypes across geographical areas. The multi-tool approach provides a valuable resource for future studies on the effects of artificial selection on livestock genomes.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"285"},"PeriodicalIF":3.5,"publicationDate":"2025-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11929999/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143691015","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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-wide identification of the NAC family genes of adzuki bean and their roles in rust resistance through jasmonic acid signaling.","authors":"Liu Shengmiao, Ding Xin, Li Yue, Yin Lihua, Ke Xiwang, Zuo Yuhu","doi":"10.1186/s12864-025-11478-0","DOIUrl":"10.1186/s12864-025-11478-0","url":null,"abstract":"<p><strong>Background: </strong>Adzuki bean (Vigna angularis) rust, caused by the fungus Uromyces vignae, is an important disease affecting adzuki bean yield and quality. Previously, several NAC transcription factors (TFs) were induced by rust infection in a resistant adzuki bean variety, suggesting that NAC TF members may play important roles in rust resistance.</p><p><strong>Results: </strong>To further explore the functions of NAC TFs in rust resistance and to provide a reference for resistant varietal breeding, 101 NAC TFs were identified from the adzuki bean genome. The synteny analysis revealed 25 pairs of VaNACs in the genome, which exhibited whole-genome/segmental duplication. Based on the phylogenetic relationships and conserved motif characteristics, the NAC TFs of V. angularis can be divided into 16 subfamilies. Previous transcriptome data showed that nine VaNACs are significantly induced by rust infection. Here, a cis-acting element analysis of these nine genes revealed that most contain hormone responsive elements, such as abscisic acid and methyl jasmonate (MeJA). The expression levels of these nine VaNACs were dynamically regulated in response to exogenous MeJA treatment, as revealed by quantitative real-time PCR analysis. Among them, seven VaNACs exhibited significantly upregulated expression, peaking at 12 h post treatment (hpt) and remaining significantly higher than that of the untreated control group for 48 hpt. These results suggest that these VaNACs are responsive to MeJA signaling and may play roles in the early and sustained transcriptional regulation of stress-related pathways. The exogenous MeJA decreased rust severity on adzuki bean leaves by 45.68%. Additionally, the expression levels of these nine genes in adzuki bean leaves in response to rust infection after pretreatment with MeJA were investigated. The expression of VaNAC002 rapidly peaked at 24 h post inoculation (hpi) and remained significantly higher than the control from 120 to 192 hpi. Subsequently, transient overexpression of VaNAC002 significantly enhanced the resistance of tobacco to Botrytis cinerea, indicating that VaNAC002 positively regulates plant disease resistance.</p><p><strong>Conclusion: </strong>These findings suggest that adzuki bean NAC family members may play important roles in disease resistance through JA signaling, with VaNAC002 having a positive regulatory role in plant immunity.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"283"},"PeriodicalIF":3.5,"publicationDate":"2025-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11929360/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143690991","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Large-scale integration of meta-QTL and genome-wide association study identifies genomic regions and candidate genes for photosynthetic efficiency traits in bread wheat.","authors":"Ming Chen, Tao Chen, Letong Yun, Zhuo Che, Jingfu Ma, Binxue Kong, Jiangying Long, Chunhua Cheng, Kaiqi Guo, Peipei Zhang, Lijian Guo, Delong Yang","doi":"10.1186/s12864-025-11472-6","DOIUrl":"10.1186/s12864-025-11472-6","url":null,"abstract":"<p><strong>Background: </strong>Improving photosynthetic efficiency is an essential strategy for advancing wheat breeding progress. Integrating wheat genetic resources provides an opportunity to discover pivotal genomic regions and candidate genes (CGs) for photosynthetic efficiency traits in wheat.</p><p><strong>Results: </strong>A large-scale meta-QTL (MQTL) analysis was performed with 1363 initial quantitative trait loci (QTLs) for photosynthetic efficiency traits extracted from 66 independent QTL mapping studies over the past decades. Consequently, 718 initial QTLs were refined into 74 MQTLs, which were distributed on all wheat chromosomes except 1D, 3 A, 4B, and 5B. Compared with the confidence interval (CI) of the initial QTL, the CI of the identified MQTL was 0.03 to 10.97 cM, with an average of 1.46 cM, which was 20.46 times narrower than that of the original QTL. The maximum explained phenotypic variance (PVE) of the MQTL ranged from 7.43 to 20.42, with an average of 11.97, which was 1.07 times higher than that of the original QTL. Of these, 54 MQTLs were validated using genome-wide association study (GWAS) data from different natural populations in previous research. A total of 3,102 CGs were identified within the MQTL intervals, where 342 CGs share homology with rice, and 1,043 CGs are highly expressed in leaves, spikes, and stems. These CGs were mainly involved in porphyrin metabolism, glyoxylate, dicarboxylate metabolism, carbon metabolism and photosynthesis antenna proteins metabolism pathways by the in silico transcriptome assessment. For the key CG TaGGR-6A (TraesCS6A02G307700) involved in the porphyrin metabolism pathway, a functional kompetitive allele-specific PCR (KASP) marker was developed at 2464 bp (A/G) position within the 3' untranslated region, successfully distinguishing two haplotypes: TaGGR-6A-Hap I (type AA) and TaGGR-6A-Hap II (type GG). Varieties with the TaGGR-6A-Hap II allele exhibited approximately 13.42% and 11.45% higher flag leaf chlorophyll content than those carrying the TaGGR-6A-Hap I allele. The elite haplotype TaGGR-6A-Hap II was positively selected during wheat breeding, as evidenced by the geographical and annual frequency distributions of the two TaGGR-6A haplotypes.</p><p><strong>Conclusion: </strong>The findings will give further insights into the genetic determinants of photosynthetic efficiency traits and provide some reliable MQTLs and putative CGs for the genetic improvement of photosynthetic efficiency in wheat.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"284"},"PeriodicalIF":3.5,"publicationDate":"2025-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11929995/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143691013","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Altered structural and transporter-related gene expression patterns in the placenta play a role in fetal demise during Porcine reproductive and respiratory syndrome virus infection.","authors":"Angelica Van Goor, Alex Pasternak, Kristen E Walker, Shannon Chick, John C S Harding, Joan K Lunney","doi":"10.1186/s12864-025-11397-0","DOIUrl":"10.1186/s12864-025-11397-0","url":null,"abstract":"<p><strong>Background: </strong>Porcine reproductive and respiratory syndrome virus (PRRSV) can be transmitted across the maternal-fetal-interface from an infected gilt to her fetuses. Although fetal infection status and disease outcomes vary, the mechanisms are not completely understood. The objective was to assess targeted placental structural and transporter-related gene expression patterns. At day 85 of gestation pregnant pigs were challenged with PRRSV, and at 12 days post maternal infection sows and fetuses were sacrificed, and the placental tissue was collected. Grouping of fetuses was by preservation status and PRRS viral load (VL): control (CTRL, n = 14), viable and low VL fetus (VIA_LVF, n = 15), viable and high VL fetus (VIA_HVF, n = 21), meconium mild and low VL fetus (MECm_LVF, n = 14), meconium mild and high VL fetus (MECm_HVF, n = 14), and meconium severe and high VL fetus (MECs_HVF, n = 13). NanoString was used to evaluate the expression of 86 genes: actin cytoskeleton signaling, arachidonic acid pathway, integrin signaling, intercellular junctions, transporters, and VEGF signaling. Statistical analyses were performed using Limma with P ≤ 0.05 considered significant.</p><p><strong>Results: </strong>We identified 1, 7, 0, 29, and 39 differentially expressed genes in VIA_LVF, VIA_HVF, MECm_LVF, MECm_HVF, and MECs_HVF, respectively, contrasted to CTRL. Placental transporter genes were significantly impacted (i.e., downregulation of SLC1A3, SLC1A5, SLC2A1, SLC2A3, SLC2A5, SLC2A10, SLC2A12, SLC7A4, SLC16A5, SLC16A10, and SLC27A6; and upregulation of SLC2A2, SLC16A3, and SLC27A4), compared to CTRL. Actin cytoskeleton signaling (ARHGEF6 and ARHGEF7), arachidonic acid (PTGES3 and PTGIS), integrin signaling (FN1 and ITGB6), intercellular junctions (CDH3 and CDH11), and VEGF signaling (MAPK3 and HPSE) gene groupings were significantly impacted, compared to CTRL.</p><p><strong>Conclusion: </strong>Data reported here indicate that fetal PRRSV infection levels rather than fetal demise is necessary for transcriptional dysregulation of the fetal placenta, with a tendency towards more downregulation in the target gene sets among susceptible fetuses. These results generally support that in susceptible fetuses there is altered solute transportation, placental structural integrity, and reduced angiogenesis. The data described here is associated with fetal PRRS resistance/resilience and susceptibility.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"279"},"PeriodicalIF":3.5,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11927291/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143676634","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}