Gene最新文献

{"title":"A multi-modal molecular characterization of the Philadelphia translocation featuring long read sequencing","authors":"Janet Hei Yin Law ,&nbsp;Chun Hang Au ,&nbsp;Amy Wing-Sze Leung ,&nbsp;Henry C.M. Leung ,&nbsp;Elaine Y.L. Wong ,&nbsp;Beca B.K. Ip ,&nbsp;Dona N.Y. Ho ,&nbsp;Shing Yan Ma ,&nbsp;Helen M.H. Chan ,&nbsp;Edmond K.W. Chiu ,&nbsp;James C.S. Chim ,&nbsp;Raymond H.S. Liang ,&nbsp;Thomas S.K. Wan ,&nbsp;Edmond S.K. Ma","doi":"10.1016/j.gene.2025.149370","DOIUrl":"10.1016/j.gene.2025.149370","url":null,"abstract":"<div><h3>Objective</h3><div>Clinically significant structural variation (SV), notably chromosomal translocation, results in the formation of fusion genes that drive leukaemogenesis. Detection of SVs is vital in clinical diagnosis, prognosis and therapy of haematological malignancies. Current methods for SV identification are low in sensitivity for cryptic cases and time-consuming for complex cases. This study investigated the feasibility of long read sequencing as an approach for SV detection and precise breakpoint characterization.</div></div><div><h3>Methods</h3><div>Six archival samples, including 4 bone marrow blood samples (F/66 B-ALL, F/25 B-ALL, M/53 CML, F/34 B-ALL) and 1 cytogenetic cell pellet each in cell culture medium (M/52 CML) or Carnoy’s fixative (M/44 CML) with known and previously characterized <em>BCR::ABL1</em> fusion transcript were selected for study. The genomic DNA was extracted from each case for further breakpoint characterization by long read sequencing (MinION R9.4.1 flow cell, Oxford Nanopore Technologies, UK).</div></div><div><h3>Results</h3><div>All the genomic breakpoints were concordant with the RNA fusion transcript breakpoints. Three typical (e1a2, e13a2, and e14a2) and 3 variant (e23a2Ins52, e8a2, and e13a2ins74) <em>BCR</em> breakpoints were identified.</div></div><div><h3>Conclusion</h3><div>Using the Ph translocation as an example, long read sequencing is a promising alternative method to detect SV, revolutionizing detection of chromosomal translocation to a higher precision. A more comprehensive spectrum of SV can be resolved along with cytogenetic results, enabling precise diagnosis and personalized monitoring of haematological malignancies.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"950 ","pages":"Article 149370"},"PeriodicalIF":2.6,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143537058","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":"Corrigendum to “PWWP2A/B: Prominent players in the proteomic landscape” [Gene 942 (2025) 149245]","authors":"Saravanaraman Ponne ,&nbsp;Raj Kumar Chinnadurai ,&nbsp;Rajender Kumar ,&nbsp;Aman Kumar Mohanty ,&nbsp;Raimunda Sâmia Nogueira Brilhante ,&nbsp;Trinh Thi Trang Nhung ,&nbsp;Sudhakar Baluchamy","doi":"10.1016/j.gene.2025.149344","DOIUrl":"10.1016/j.gene.2025.149344","url":null,"abstract":"","PeriodicalId":12499,"journal":{"name":"Gene","volume":"948 ","pages":"Article 149344"},"PeriodicalIF":2.6,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143537060","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":"Revealing the key aromatic compounds in Malus ’Lollipop’ flowers by transcriptome and metabolome","authors":"Qin Peng ,&nbsp;Limeng Zhou ,&nbsp;Qingqing Xiong ,&nbsp;Fangyuan Yu ,&nbsp;Wangxiang Zhang ,&nbsp;Junjun Fan","doi":"10.1016/j.gene.2025.149371","DOIUrl":"10.1016/j.gene.2025.149371","url":null,"abstract":"<div><div>The ornamental crabapple <em>Malus</em> (<em>M.</em>) ’Lollipop’ is renowned for its compact growth and fragrant flowers. This study aims to elucidate the biosynthesis molecular mechanism of volatile organic compounds (VOCs) across four developmental stages of the <em>M.</em> ’Lollipop’ flowers using metabolomics and transcriptomics analyses. Gas chromatography-mass spectrometry (GC–MS) identified 29 VOCs (aliphatic derivatives, benzenes, and alkanes) in <em>M.</em> ’Lollipop’ flowers. Orthogonal Partial Least Squares Discriminant Analysis (OPLS-DA) analysis highlights 14 key differential aromatic compounds (VIP ≥ 1), featuring (Z)-3-hexen-1-yl acetate in stage 1, methyl benzoate in stage 2, benzyl alcohol and linalool in stage 3, and camphene and (Z)-3-hexen-1-ol in stage 4. (Z)-3-hexen-1-yl acetate was identified as a co-primary constituent in the four flowering stages, designated as a key and floral contributing metabolite (variable importance in projection (VIP) ≥ 1&amp; odor activity value (OAV) ≥ 1). RNA sequencing revealed key genes including CAT, DXS, MVD, HMGCR, FDPS, and TPSc in camphene and linalool synthesis, aroA, ADT, PDT, PAL, BEBT1, SDR, 4CL, CNL, and BALDH for benzyl alcohol, benzaldehyde, and methyl benzoate production. And PLA2G, SPLA2, TGL4, LOX2S and ADH1 in (Z)-3-hexen-1-yl acetate and (Z)-3-hexen-1-ol synthesis. 24 transcription factors (TFs) were predicted to be closely linked to genes involved in VOC synthesis. The findings above deepen our comprehension of the floral scent in crabapple, laying a foundation for further investigations into their functions and potential industrial applications.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"951 ","pages":"Article 149371"},"PeriodicalIF":2.6,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143537062","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":"Unraveling the role of miR-767 in tumor progression: Mechanisms and clinical implications","authors":"Zheng Fu ,&nbsp;Chenghong Jin ,&nbsp;Sihan Yu ,&nbsp;Hening Xu ,&nbsp;Haoyu Zhang ,&nbsp;Mingxiao Qiu ,&nbsp;Jingyin Dong ,&nbsp;Shiwei Duan","doi":"10.1016/j.gene.2025.149366","DOIUrl":"10.1016/j.gene.2025.149366","url":null,"abstract":"<div><div>MicroRNAs (miRNAs), a distinctive class of small single-stranded non-coding RNA molecules typically spanning between 21 and 23 nucleotides, hold a pivotal position within the intricate regulatory network governing gene expression. Notably, miR-767, located on chromosome Xq28, has emerged as a significant player in tumor development, with its two mature products, miR-767-3p and miR-767-5p, garnering considerable attention in scientific inquiry. Extensive investigations reveal aberrant expression patterns of miR-767 across a spectrum of cancers affecting neurological, digestive, reproductive, urinary, and respiratory systems. Remarkably, miR-767 exhibits substantial upregulation in 13 distinct cancer types and demonstrates precise targeting of at least 14 pivotal protein-coding genes (PCGs) crucial for regulating cellular processes including the cell cycle, proliferation, epithelial-mesenchymal transition (EMT), invasion, and migration. Moreover, the expression level of miR-767 bears significant implications for cancer patient diagnosis, prognosis, and drug sensitivity, thus offering novel insights for clinical tumor management. At the mechanistic level, miR-767-5p and miR-767-3p intricately participate in the regulation of key signaling pathways, with miR-767-5p influencing JAK/STAT, EPK1/2, and PI3K/Akt pathways, while miR-767-3p predominantly affects TGF-β and PI3K/Akt pathways. Notably, both miRNAs converge on the PI3K/Akt pathway, underscoring its pivotal role in their joint regulation. This review provides a comprehensive analysis of the intricate mechanisms underlying miR-767-mediated tumor progression through the modulation of diverse target genes, and explores the potential correlation between host gene GABRA3 transcription and the expression of these miRNAs. Furthermore, the review systematically delineates the binding sites of miR-767-5p and miR-767-3p with circRNA and target genes, alongside the PCGs regulated by miR-767, offering profound insights into their multifaceted roles in tumor development. In essence, this review not only comprehensively elucidates the pivotal role of miR-767 in tumor progression but also provides valuable cues and avenues for future research, thereby fostering deeper scientific inquiry within the realm of cancer research.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"949 ","pages":"Article 149366"},"PeriodicalIF":2.6,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143526749","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":"Late embryogenesis abundant gene GhLEA-5 of semi-wild cotton positively regulates salinity tolerance in upland cotton","authors":"Chunyan Tian ,&nbsp;Abdul Rehman ,&nbsp;Xiaoyang Wang ,&nbsp;Zhenzhen Wang ,&nbsp;Hongge Li ,&nbsp;Jun Ma ,&nbsp;Xiongming Du ,&nbsp;Zhen Peng ,&nbsp;Shoupu He","doi":"10.1016/j.gene.2025.149372","DOIUrl":"10.1016/j.gene.2025.149372","url":null,"abstract":"<div><div>The productivity and quality of cotton are significantly compromised by salt stress. In this study, the full length of encoding region and genomic DNA sequences of <em>GhLEA_5A/D</em> (<em>Gh_A10G166600</em> and <em>Gh_D10G188300</em>), which belong to the late embryogenesis abundant gene family in allotetraploid upland cotton (<em>Gossypium hirsutum L.</em>) and semi-wild cotton (<em>Gossypium purpurascens</em>), were isolated and their salt tolerance was experimentally confirmed. Analysis of sequence alignments and phylogenetic trees indicated a significant level of homology between <em>GhLEA-5A</em> and <em>GhLEA-5D</em>. Additionally, a conserved protein motif was consistently identified across these sequences. The transcriptome data analysis showed that the expression level of <em>GhLEA-5A/D</em> was substantially enhanced in the leaves of salt-tolerant <em>G. purpurascens</em> accessions compared to salt-sensitive materials. In the real-time quantitative reverse transcription PCR (qRT-PCR) assays, notable expression levels of the <em>GhLEA-5D</em> gene were detected in salt-tolerant upland cotton materials following exposure to salt stress at 3 and 12-hour time points. The suppression of <em>GhLEA-5A/D</em> transcription via Virus-induced Gene Silencing (VIGS) technology significantly exacerbates salt sensitivity in cotton. This is evidenced by the nearly 50 % increase in malondialdehyde (MDA) content alongside a 60 % reduction in peroxidase (POD) levels in salt-treated plants when compared to the control group. The overexpression of the GhLEA-5A/D gene conferred enhanced salt tolerance in Arabidopsis, resulting in a 25 % increase in root length, a 30 % improvement in survival rate, a 15 % increase in water retention, and a 15 % boost in photosynthetic efficiency. The chlorophyll fluorescence parameters, enzyme activities, diaminobenzine, and nitroblue tetrazolium staining suggested that <em>GhLEA-5A/D</em> likely exhibited a positive regulatory role for cotton responding to salt stress. Furthermore, we identified 76 candidate proteins that potentially interact with <em>GhLEA-5</em> in the yeast two-hybrid screening library. These results provide a theoretical basis for studying the mechanism of cotton salt tolerance and offer new resources for improving cotton salt tolerance genes.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"949 ","pages":"Article 149372"},"PeriodicalIF":2.6,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143529035","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":"Computational and mathematical genomics of coronaviruses","authors":"Sk. Sarif Hassan ,&nbsp;Debaleena Nawn ,&nbsp;Vladimir N. Uversky","doi":"10.1016/j.gene.2025.149373","DOIUrl":"10.1016/j.gene.2025.149373","url":null,"abstract":"","PeriodicalId":12499,"journal":{"name":"Gene","volume":"951 ","pages":"Article 149373"},"PeriodicalIF":2.6,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143531292","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":"Epigenetic activation of PTEN by valproic acid inhibits PI3K/AKT signaling and Burkitt lymphoma cell growth","authors":"Chuntuan Li ,&nbsp;Shengquan Liu ,&nbsp;Jingjing Gao ,&nbsp;Yahong Xu ,&nbsp;Qunyi Peng ,&nbsp;Dan Weng ,&nbsp;Dan Wang ,&nbsp;Wanlin Yang ,&nbsp;Ping Yi ,&nbsp;Zuopeng Lin ,&nbsp;Jinting Chen","doi":"10.1016/j.gene.2025.149369","DOIUrl":"10.1016/j.gene.2025.149369","url":null,"abstract":"<div><div>Histone deacetylase (HDAC) inhibitors show promise in treating Burkitt lymphoma (BL), although the precise mechanisms remain unclear. We investigated the effects of valproic acid (VPA), a specific HDAC inhibitor, on BL cell lines RAJI and CA46, focusing on the PTEN/PI3K/AKT pathway. Cell viability, cell cycle progression, and apoptosis were evaluated using the Cell Counting Kit-8 assay and the Annexin V-fluorescein isothiocyanate assay. Chromatin immunoprecipitation sequencing (ChIP-seq) assessed acetylation at the PTEN promoter, while gene expression and protein levels were measured via reverse transcription quantitative polymerase chain reaction and Western blotting, respectively. VPA treatment significantly reduced BL cell viability and induced apoptosis and cell cycle arrest in a dose-dependent manner. Compared to peripheral blood mononuclear cells, BL cells exhibited significantly higher HDAC mRNA and protein levels. ChIP-seq analysis revealed increased acetylation of the PTEN promoter following exposure to VPA. After treatment with 4 mM VPA, PTEN protein levels in BL cells increased significantly, while levels of HDAC, p-AKT, and p-p70S6K proteins decreased markedly. Furthermore, compared to VPA treatment alone, the combination of VPA and the PI3K inhibitor BEZ235 led to even greater PTEN protein expression, further decreased p-AKT and p-p70S6K protein levels, and further reduced cell viability in BL cells. VPA exerts its antitumor effects in BL cells by modulating the PTEN/PI3K/AKT pathway through the inhibition of HDAC1.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"950 ","pages":"Article 149369"},"PeriodicalIF":2.6,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143531296","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":"Crucial role of preserving umbilical cord stumps for genetic decoding of a family with rhabdoid tumor predisposition syndrome","authors":"Murugasamy Pradeepkumar ,&nbsp;Vignesh Kandhakumar ,&nbsp;Muniasamy Saravanan ,&nbsp;Mohandass Kaviya ,&nbsp;Mohan Gomathi","doi":"10.1016/j.gene.2025.149353","DOIUrl":"10.1016/j.gene.2025.149353","url":null,"abstract":"<div><h3>Background</h3><div>The Rhabdoid tumor is an aggressive tumor that is commonly found in infants and children with a prevalence of about, 0.6 in every 1 million children. The <em>SMARCB1</em> or <em>SMARCA4</em> gene mutations can result in Rhabdoid tumor predisposition syndrome 1 and 2 respectively. In Indian customs, dried umbilical cord stumps that had fallen off were stored to treat various illnesses, including infertility.</div></div><div><h3>Aim and objective</h3><div>This study aims to unravel the mystery behind recurrent childhood loss in a family using umbilical cord stumps of the deceased children.</div></div><div><h3>Methodology</h3><div>We obtained the dried umbilical cord stumps of the deceased children, which were stored by their parents, as there was no genetic diagnosis performed on the children who passed away unexpectedly. Following DNA extraction from the parents’ and the umbilical cord stumps, whole exome sequencing analysis (WES) was performed.</div></div><div><h3>Results</h3><div>The WGS report showed a pathogenic germline mutation, Chr22:g.23791780; c.118C &gt; T; (p.Arg40Ter) in the <em>SMARCB1</em> gene causing Rhabdoid tumor predisposition syndrome 1, which was present in the children who passed away earlier. The mother was discovered to be a silent carrier with heterozygous mutant alleles, according to carrier screening and segregation analysis. Genetic counseling was given to the parents in light of the 50 % recurring risk in the foetus, and the continued pregnancy was determined to be normal. The diagnostic benefit of using dried umbilical cord stumps which are customarily retained by Indian parents who have had early childhood losses was demonstrated by this investigation.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"948 ","pages":"Article 149353"},"PeriodicalIF":2.6,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143508355","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":"Association of genetic variation in the leptin-melanocortin system with drive for thinness in patients with eating disorders: A pilot study","authors":"Laura González-Rodríguez ,&nbsp;Luz María González ,&nbsp;Angustias García-Herráiz ,&nbsp;Sonia Mota-Zamorano ,&nbsp;Isalud Flores ,&nbsp;Guillermo Gervasini","doi":"10.1016/j.gene.2025.149364","DOIUrl":"10.1016/j.gene.2025.149364","url":null,"abstract":"<div><div>We aimed to investigate whether genetic variants in the leptin-melanocortin system involved in anorexigenic signaling influence personality dimensions and psychopathological symptoms in eating disorders (ED) patients. The population consisted of 309 ED patients [221 with anorexia nervosa (AN) and 88 with bulimia nervosa (BN)] and 396 healthy controls. Patients underwent psychometric assessment using the Eating Disorders Inventory Test-2 (EDI-2) and the Symptom Checklist 90 Revised (SCL-90R) questionnaires. Fourteen tag-SNPs in the <em>LEP</em>, <em>POMC</em>, and <em>MC4R</em> genes, were determined. <em>Drive for thinness</em> (DT) was significantly affected by genetic variability. After correction for multiple testing, regression models showed that AN patients carrying the <em>LEP</em> rs11761556 CC variant genotype scored higher in this scale than AA/CA carriers did [mean difference = 4.43 (2.18–6.68), p &lt; 0.001], although the significance was restrained to the restrictive subtype [4.92 (2.00–7.83), p = 0.001]. BN patients with the <em>LEP</em> rs10954173 AA genotype displayed lower scores [-8.7 (−12.31--3.91); p &lt; 0.001]. Finally, gene-gene interaction analyses revealed two SNP pairs associated with body-mass index in AN patients (<em>LEP</em>rs3828942-<em>POMC</em>rs1009388, p &lt; 0.001 and <em>LEP</em> rs11763517-<em>POMC</em>rs1009388, p = 0.002). Regarding DT scores, the <em>POMC</em>rs6545975-<em>LEP11763517</em> SNP pair showed the strongest effect (p &lt; 0.001) in AN<strong>.</strong> Genetic variants in the leptin-melanocortin system, may interact to influence personality dimensions in ED patients, which highlights the importance of considering genetic factors in the pathophysiology of these disorders.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"949 ","pages":"Article 149364"},"PeriodicalIF":2.6,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143509167","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":"Divergent adaptation to highland and tropical environments in Bolivian Creole cattle","authors":"Olivia Marcuzzi ,&nbsp;Paulo Álvarez Cecco ,&nbsp;Leónidas H. Olivera ,&nbsp;Juan A. Pereira Rico ,&nbsp;Francisco Calcaterra ,&nbsp;Ariel Loza Vega ,&nbsp;Pilar Peral-García ,&nbsp;María E. Fernández ,&nbsp;Andrés Rogberg Muñoz ,&nbsp;Guillermo Giovambattista","doi":"10.1016/j.gene.2025.149354","DOIUrl":"10.1016/j.gene.2025.149354","url":null,"abstract":"<div><div>Bolivian Creole cattle populations evolved under low levels of breeding management and, during more than 500 years of natural selection, became adapted to various environments such as the contrasting highland and subtropical environments. Recently, highland Creole cattle were crossbred with Holstein to improve dairy production. The aim of this research was to evaluate the divergent adaptation through selection footprints of Bolivian Creole cattle from Andean highland and tropical lowlands, and to evaluate the effect of Holstein introgression in highland Creole. For this purpose, 130 Creole cattle (75 highland, 55 lowland) and 88 Holstein were genotyped using a microarray. The database was used to determine population structure and admixture and detect selection sweeps using F_ST, Rsb, XP-EHH, and ROH. Ancestry inference suggested that selection peaks were not due to Holstein introgression. The NCBI database was used to retrieve genes from the common regions and then perform gene ontology analysis. The most prominent selection peaks were on BTA20 and BTA23 and included the <em>PRLR</em> (slick phenotype) and <em>Class I</em> and <em>IIa BoLA</em> genes. Other windows contained candidate genes for hypoxia (<em>ANXA2</em>, <em>NDUFA4L2</em>), angiogenesis and haematological parameters (<em>ANXA2</em>, <em>CPLANE1</em>, <em>NRP1</em>, <em>NRP2</em>), immune response (<em>IL7R</em>, <em>IL6ST</em>, <em>IL31RA</em>, <em>C6</em>, <em>C7, STAT6</em>, <em>NKG2A</em>, <em>IRAK4</em>, <em>KLR, CLEC</em>), oxidative stress (<em>GSTA, HSD17B6</em>) and morphological traits (<em>PLAG1, CHCHD7</em>, <em>CAP2, ARL15)</em>. GO analysis revealed enrichment terms and pathways related to immune response, glutathione and retinol metabolism and reported QTLs for coat characteristics, immune response and tick resistance. The results suggest the complex mechanism in the adaptation of Bolivian Creole cattle to the contrasting highland and subtropical environments.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"949 ","pages":"Article 149354"},"PeriodicalIF":2.6,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143523092","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}