Frontiers in Genetics最新文献

{"title":"BIMSSA: enhancing cancer prediction with salp swarm optimization and ensemble machine learning approaches.","authors":"Pinakshi Panda, Sukant Kishoro Bisoy, Amrutanshu Panigrahi, Abhilash Pati, Bibhuprasad Sahu, Zheshan Guo, Haipeng Liu, Prince Jain","doi":"10.3389/fgene.2024.1491602","DOIUrl":"10.3389/fgene.2024.1491602","url":null,"abstract":"<p><strong>Background: </strong>Cancer rates are rising rapidly, causing global mortality. According to the World Health Organization (WHO), 9.9 million people died from cancer in 2020. Machine learning (ML) helps identify cancer early, reducing deaths. An ML-based cancer diagnostic model can use the patient's genetic information, such as microarray data. Microarray data are high dimensional, which can degrade the performance of the ML-based models. For this, feature selection becomes essential.</p><p><strong>Methods: </strong>Swarm Optimization Algorithm (SSA), Improved Maximum Relevance and Minimum Redundancy (IMRMR), and Boruta form the basis of this work's ML-based model BIMSSA. The BIMSSA model implements a pipelined feature selection method to effectively handle high-dimensional microarray data. Initially, Boruta and IMRMR were applied to extract relevant gene expression aspects. Then, SSA was implemented to optimize feature size. To optimize feature space, five separate machine learning classifiers, Support Vector Machine (SVM), Random Forest (RF), Extreme Learning Machine (ELM), AdaBoost, and XGBoost, were applied as the base learners. Then, majority voting was used to build an ensemble of the top three algorithms. The ensemble ML-based model BIMSSA was evaluated using microarray data from four different cancer types: Adult acute lymphoblastic leukemia and Acute myelogenous leukemia (ALL-AML), Lymphoma, Mixed-lineage leukemia (MLL), and Small round blue cell tumors (SRBCT).</p><p><strong>Results: </strong>In terms of accuracy, the proposed BIMSSA (Boruta + IMRMR + SSA) achieved 96.7% for ALL-AML, 96.2% for Lymphoma, 95.1% for MLL, and 97.1% for the SRBCT cancer datasets, according to the empirical evaluations.</p><p><strong>Conclusion: </strong>The results show that the proposed approach can accurately predict different forms of cancer, which is useful for both physicians and researchers.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"15 ","pages":"1491602"},"PeriodicalIF":2.8,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11743448/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143004432","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":"Identification of key genes affecting intramuscular fat deposition in pigs using machine learning models.","authors":"Yumei Shi, Xini Wang, Shaokang Chen, Yanhui Zhao, Yan Wang, Xihui Sheng, Xiaolong Qi, Lei Zhou, Yu Feng, Jianfeng Liu, Chuduan Wang, Kai Xing","doi":"10.3389/fgene.2024.1503148","DOIUrl":"10.3389/fgene.2024.1503148","url":null,"abstract":"<p><p>Intramuscular fat (IMF) is an important indicator for evaluating meat quality. Transcriptome sequencing (RNA-seq) is widely used for the study of IMF deposition. Machine learning (ML) is a new big data fitting method that can effectively fit complex data, accurately identify samples and genes, and it plays an important role in omics research. Therefore, this study aimed to analyze RNA-seq data by ML method to identify differentially expressed genes (DEGs) affecting IMF deposition in pigs. In this study, a total of 74 RNA-seq data from muscle tissue samples were used. A total of 155 DEGs were identified using a limma package between the two groups. 100 and 11 significant genes were identified by support vector machine recursive feature elimination (SVM-RFE) and random forest (RF) models, respectively. A total of six intersecting genes were in both models. KEGG pathway enrichment analysis of the intersecting genes revealed that these genes were enriched in pathways associated with lipid deposition. These pathways include α-linolenic acid metabolism, linoleic acid metabolism, ether lipid metabolism, arachidonic acid metabolism, and glycerophospholipid metabolism. Four key genes affecting intramuscular fat deposition, <i>PLA2G6, MPV17, NUDT2</i>, and <i>ND4L</i>, were identified based on significant pathways. The results of this study are important for the elucidation of the molecular regulatory mechanism of intramuscular fat deposition and the effective improvement of IMF content in pigs.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"15 ","pages":"1503148"},"PeriodicalIF":2.8,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11743517/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143004133","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":"A breeding method for Ogura CMS restorer line independent of restorer source in <i>Brassica napus</i>.","authors":"Xuesong Wang, Xingyu Liang, Rui Wang, Yuan Gao, Yun Li, Haoran Shi, Wanzhuo Gong, Saira Saleem, Qiong Zou, Lanrong Tao, Zeming Kang, Jin Yang, Qin Yu, Qiaobo Wu, Hailan Liu, Shaohong Fu","doi":"10.3389/fgene.2024.1521277","DOIUrl":"10.3389/fgene.2024.1521277","url":null,"abstract":"<p><p>The Ogura cytoplasmic male sterility (CMS) line of <i>Brassica napus</i> has gained significant attention for its use in harnessing heterosis. It remains unaffected by temperature and environment and is thorough and stable. The Ogura cytoplasmic restorer line of <i>Brassica napus</i> is derived from the distant hybridization of <i>Raphanus sativus L.</i> and <i>B. napus</i>, but it carried a large number of radish fragments into <i>Brassica napus</i>, because there is no homologous allele of the restorer gene in <i>B. napus</i>, transferring it becomes challenging. In this study, the double haploid induction line in <i>B. napus</i> was used as the male parent for hybridization with the Ogura CMS of <i>B. napus.</i> Surprisingly, fertile plants appeared in the offspring. Further analysis revealed that the cytoplasmic type, ploidy, and chromosome number of the fertile offspring were consistent with the sterile female parent. Moreover, the mitochondrial genome similarity between the fertile offspring and the sterile female parent was 97.7% indicates that the cytoplasm of the two is the same, while the nuclear gene difference between fertile offspring and sterile female parent was only 10.33%, indicates that new genes appeared in the offspring. To further investigate and locate the restorer gene, the BSA method was employed to construct extreme mixed pools. As a result, the restorer gene was mapped to three positions: A09 chromosome 10.99-17.20 Mb, C03 chromosome 5.07-5.34 Mb, and C09 chromosome 18.78-36.60 Mb. The experimental results have proved that induction does produce restorer genes. The induction of the Ogura CMS restorer gene through DH induction line provides a promising new approach for harnessing heterosis in <i>B. napus</i>.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"15 ","pages":"1521277"},"PeriodicalIF":2.8,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11743515/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143004398","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":"Evaluation of controls, quality control assays, and protocol optimisations for PacBio HiFi sequencing on diverse and challenging samples.","authors":"Iraad F Bronner, Emma Dawson, Naomi Park, Olaf Piepenburg, Michael A Quail","doi":"10.3389/fgene.2024.1505839","DOIUrl":"10.3389/fgene.2024.1505839","url":null,"abstract":"<p><p>The Darwin Tree of Life (DToL) project aims to generate high-quality reference genomes for all eukaryotic organisms in Britain and Ireland. At the time of writing, PacBio HiFi reads are generated for all samples using the Sequel IIe systems by the Wellcome Sanger Institute's Scientific Operations teams, however we expect lessons from this work to apply directly to the Revio system too, as core principles of SMRT sequencing remain the same. We observed that HiFi yield is highly variable for DToL samples. We have investigated what drives this variation, and potential mitigations. To support these investigations a number of controls were evaluated to ensure that the library and sequencing preparation procedures, reagents, consumables, and Sequel IIe instruments, were performing as expected. Our findings support that a primary factor driving variability in HiFi yield is the quality of the DNA prior to library construction, e.g., purity, size, and damage. We investigated whether quality assessment assays could link measurable DNA damage or purity to sequencing yield. Some correlation could be established, however no assay was predictive of sequencing yield for all samples, indicating that the variability is driven by multiple factors that may interact. We demonstrate that contaminants present in some samples are the cause of very low HiFi yield, and show that these contaminants can negatively affect the PacBio internal sequencing control and samples multiplexed on the same SMRT Cell. We found that consistently high yields could be obtained if an amplification workflow was utilised, namely PacBio's ultra-low input library preparation protocol.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"15 ","pages":"1505839"},"PeriodicalIF":2.8,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11752452/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143023023","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":"Insights from social media into public perspectives on investigative genetic genealogy.","authors":"Sara Huston, Diana Madden, Andrea Villanes, Nathan Reed, Whitney Bash Brooks, Christopher Healey, Christi Guerrini","doi":"10.3389/fgene.2024.1482831","DOIUrl":"https://doi.org/10.3389/fgene.2024.1482831","url":null,"abstract":"<p><p>Social media sites like X (formerly Twitter) increasingly serve as spaces for the public to discuss controversial topics. Social media can spark extreme viewpoints and spread biased or inaccurate information while simultaneously allowing for debate around policy-relevant topics. The arrest of Joseph J. DeAngelo in April 2018 ignited a barrage of social media conversations on how DNA and genetic genealogy led to the suspect. These conversations continued over the following years as policies changed and as the use of the approach expanded. We examined social media coverage of investigative genetic genealogy (IGG) to characterize the volume and temporal patterns in the topics and sentiments of these public conversations. First, using a data analytics tool Brandwatch Consumer Research, we built flexible search strings to collect tweets from the social media platform Twitter/X for IGG-relevant content published from 2018 to 2022, resulting in 24,209 tweets. Second, we applied informatics tools to the dataset to generate topic clusters and analyze trends in cluster volume and distribution over time to define the top 25 peaks in tweet volume, representing the 25 events that generated the highest volume of conversation over the 5-year period. Third, drawing on the contextual framework of key IGG events, we selected three of the top ten events to code for sentiment along with a randomly sampled subset of tweets across the timeframe. Qualitative coding for position on IGG revealed a majority of tweets were supportive of the use of IGG, but key concerns were also voiced about the ethics of IGG. Over a third of conversations on Twitter/X were on either cases solved or suggestions for use of IGG. We archived the social media data for future research. These data highlight key areas of public support and concern within IGG processes and across application contexts.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"15 ","pages":"1482831"},"PeriodicalIF":2.8,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11743634/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143004062","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":"An investigation of a hemophilia A female with heterozygous intron 22 inversion and skewed X chromosome inactivation.","authors":"Xiaoyan Tan, Yi Yang, Xia Wu, Jing Zhu, Teng Wang, Huihui Jiang, Shu Chen, Shifeng Lou","doi":"10.3389/fgene.2024.1500167","DOIUrl":"10.3389/fgene.2024.1500167","url":null,"abstract":"<p><strong>Objectives: </strong>Hemophilia A (HA) is an X-linked recessive inherited bleeding disorder that typically affects men. Women are usually asymptomatic carriers, and rarely presenting with severe or moderately severe phenotype. This study aims to describe a case of a 17-year-old girl with moderate HA, investigating the mechanisms of her condition and the genetic basis within her family.</p><p><strong>Methods: </strong>We conducted coagulation tests and bleeding assessments to evaluate her bleeding phenotype. Molecular genetic examinations, karyotype analysis, X-chromosome inactivation testing, and targeted bioinformatic analysis were used to identify potential genetic etiologies.</p><p><strong>Results: </strong>The proband exhibited a severe bleeding phenotype and was found to be a heterozygous carrier of an intron 22 inversion (Inv22) with a normal chromosomal karyotype. No other hemostatic defects were identified through whole exome sequencing. The proband's mother and monozygotic twin sister are also Inv22 carriers, yet remain asymptomatic with normal FVIII activity. X-chromosome inactivation experiments revealed unbalanced inactivation in the proband, leading to the silencing of the healthy X copy. Notably, several novel X-linked gene mutations (SHROOM2, RPGR, VCX3B, GAGE, GCNA, ZNF280C, CT45A, and XK) were identified in the proband compared to her monozygotic twin sister, though their impact on X-chromosome inactivation remains unclear.</p><p><strong>Conclusion: </strong>Our findings suggest that the proband's bleeding phenotype results from unbalanced X-chromosome inactivation. This research marks the first analysis of X chromosome-related gene mutations among monozygotic twins who are carriers of hemophilia A, laying the groundwork for further investigations into the disorder's pathogenesis in women and highlighting the complexities in genetic counseling.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"15 ","pages":"1500167"},"PeriodicalIF":2.8,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11743268/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143004415","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":"Identification of a novel frameshift variation in ANKRD11: a case report of KBG syndrome.","authors":"Qing Shao, Qiang Jiang, Yuqi Luo, Yimei Meng, Guoyu Tian, Xiao Yin","doi":"10.3389/fgene.2024.1439905","DOIUrl":"10.3389/fgene.2024.1439905","url":null,"abstract":"<p><strong>Background: </strong>KBG syndrome (KBGS, OMIM: 148050) is a rare genetic disorder characterized by macrodontia, short stature, skeletal abnormalities, and neurological manifestations. The objective of this study is to investigate a case of KBG syndrome caused by a novel frameshift mutation in ANKRD11.</p><p><strong>Methods and results: </strong>We present the case of an 18-year-old Chinese male exhibiting characteristic features including a triangular face, micrognathia, hypertelorism, macrodontia, bushy eyebrows, prominent ears, short stature, low hairline, delayed cognitive development, and scoliosis. Whole exome sequencing identified a novel frameshift variant in the ANKRD11 gene which ultimately led to the diagnosis of KBG syndrome.</p><p><strong>Conclusion: </strong>In this study we have identified a previously unreported frameshift variant (NM_013275.6:c.2589dup) in ANKRD11 that causes KBG syndrome. This finding expands both the molecular and clinical spectrum of this rare genetic disease.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"15 ","pages":"1439905"},"PeriodicalIF":2.8,"publicationDate":"2025-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11739138/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143004040","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":"Association between METTL14 gene polymorphisms and risk of ovarian endometriosis.","authors":"Zijun Zhou, Youkun Jie, Xianyue Hu, Guange Chen, Yanjing Bao, Zhenbo OuYang, Liangzhi Wu, Tianyang Gao, Qiushi Zhang, Wenfeng Hua","doi":"10.3389/fgene.2024.1460216","DOIUrl":"10.3389/fgene.2024.1460216","url":null,"abstract":"<p><strong>Background: </strong>Endometriosis, a prevalent chronic gynecological condition, is frequently associated with infertility and pelvic pain. Despite numerous studies indicating a correlation between epigenetic regulation and endometriosis, its precise genetic etiology remains elusive. Methyltransferase-like 14 (METTL14), a crucial component of the N6-methyladenosine (m⁶A) RNA methyltransferase complex and an RNA binding scaffold, is known to play a pivotal role in various human diseases. The possibility that single nucleotide polymorphisms (SNPs) in the METTL14 gene contribute to susceptibility of endometriosis has not been thoroughly investigated.</p><p><strong>Methods: </strong>We assessed the genotype frequencies of five potential functional METTL14 SNPs (rs298982 G>A, rs62328061A>G, rs9884978G>A, rs4834698C>T, and rs1064034A>T) in a Chinese population consisting of 458 patients with ovarian endometriosis and 462 healthy controls. We employed unconditional logistic regression and stratified analyses to evaluate their genotypic associations with the risk of ovarian endometriosis.</p><p><strong>Results: </strong>Among the five SNPs examined, we found that the rs298982 A allele was significantly associated with increased risk, whereas the rs62328061 G allele was linked to a decreased risk of ovarian endometriosis. Individuals harboring two unfavorable genotypes demonstrated a significantly elevated risk of ovarian endometriosis (adjusted odds ratio (AOR) = 1.57, 95% confidence interval (CI) = 1.16-2.13, <i>P</i> = 0.004) compared with those with no risk genotypes. Stratified analysis revealed the risk effect of rs298982 GA/AA genotypes in the gravidity≤1, parity≤1, rASRM stage I, and rASRM stage II + III + IVsubgroups. Haplotype analysis showed that individuals with the GATAA haplotype were at higher risk of ovarian endometriosis (AOR = 5.54, 95% CI = 1.63-18.87, <i>P</i> = 0.006), whereas the AGTTG haplotype exhibited protective effects (AOR = 0.55, 95% CI = 0.31-0.97, <i>P</i> = 0.039) compared with wild-type GACAG haplotype carriers. Additionally, Bayesian false discovery probability and false positive report probability analysis confirmed the robustness of the significant findings. Expression quantitative trait loci analysis revealed a significant association between the rs9884978 GA/AA genotypes and elevated METTL14 mRNA levels in fibroblasts and adrenal gland. Conversely, the rs298982 GA/GG genotypes were significantly associated with reduced METTL14 mRNA levels in the nucleus accumbens and frontal cortex.</p><p><strong>Conclusion: </strong>Our results demonstrate that METTL14 polymorphisms are associated with susceptibility to ovarian endometriosis among Chinese women.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"15 ","pages":"1460216"},"PeriodicalIF":2.8,"publicationDate":"2025-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11739277/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143004419","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":"The value of a metabolic and immune-related gene signature and adjuvant therapeutic response in pancreatic cancer.","authors":"Danlei Ni, Jiayi Wu, Jingjing Pan, Yajing Liang, Zihui Xu, Zhiying Yan, Kequn Xu, Feifei Wei","doi":"10.3389/fgene.2024.1475378","DOIUrl":"10.3389/fgene.2024.1475378","url":null,"abstract":"<p><strong>Background: </strong>Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive malignancy characterized by a dismal prognosis. Treatment outcomes exhibit substantial variability across patients, underscoring the urgent need for robust predictive models to effectively estimate survival probabilities and therapeutic responses in PDAC.</p><p><strong>Methods: </strong>Metabolic and immune-related genes exhibiting differential expression were identified using the TCGA-PDAC and GTEx datasets. A genetic prognostic model was developed via univariable Cox regression analysis on a training cohort. Predictive accuracy was assessed using Kaplan-Meier (K-M) curves, calibration plots, and ROC curves. Additional analyses, including GSAE and immune cell infiltration studies, were conducted to explore relevant biological mechanisms and predict therapeutic efficacy.</p><p><strong>Results: </strong>An 8-gene prognostic model (AK2, CXCL11, TYK2, ANGPT4, IL20RA, MET, ENPP6, and CA12) was established. Three genes (AK2, ENPP6, and CA12) were associated with metabolism, while the others were immune-related. Most genes correlated with poor prognosis. Validation in TCGA-PDAC and GSE57495 datasets demonstrated robust performance, with AUC values for 1-, 3-, and 5-year OS exceeding 0.7. The model also effectively predicted responses to adjuvant therapy.</p><p><strong>Conclusion: </strong>This 8-gene signature enhances prognostic accuracy and therapeutic decision-making in PDAC, offering valuable insights for clinical applications and personalized treatment strategies.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"15 ","pages":"1475378"},"PeriodicalIF":2.8,"publicationDate":"2025-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11758928/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143046396","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":"Genomic selection for resistance to one pathogenic strain of <i>Vibrio splendidus</i> in blue mussel <i>Mytilus edulis</i>.","authors":"Munusamy Ajithkumar, Jonathan D'Ambrosio, Marie-Agnès Travers, Romain Morvezen, Lionel Degremont","doi":"10.3389/fgene.2024.1487807","DOIUrl":"10.3389/fgene.2024.1487807","url":null,"abstract":"<p><strong>Introduction: </strong>The blue mussel is one of the major aquaculture species worldwide. In France, this species faces a significant threat from infectious disease outbreaks in both mussel farms and the natural environment over the past decade. Diseases caused by various pathogens, particularly <i>Vibrio</i> spp., have posed a significant challenge to the mussel industry. Genetic improvement of disease resistance can be an effective approach to overcoming this issue.</p><p><strong>Methods: </strong>In this work, we tested genomic selection in the blue mussel (<i>Mytilus edulis</i>) to understand the genetic basis of resistance to one pathogenic strain of <i>Vibrio splendidus</i> (strain 14/053 2T1) and to predict the accuracy of selection using both pedigree and genomic information. Additionally, we performed a genome-wide association study (GWAS) to identify putative QTLs underlying disease resistance. We conducted an experimental infection involving 2,280 mussels sampled from 24 half-sib families containing each two full-sib families which were injected with <i>V. splendidus</i>. Dead and survivor mussels were all sampled, and among them, 348 dead and 348 surviving mussels were genotyped using a recently published multi-species medium-density 60K SNP array.</p><p><strong>Results: </strong>From potentially 23.5K SNPs for <i>M. edulis</i> present on the array, we identified 3,406 high-quality SNPs, out of which 2,204 SNPs were successfully mapped onto the recently published reference genome. Heritability for resistance to V. splendidus was moderate ranging from 0.22 to 0.31 for a pedigree-based model and from 0.28 to 0.36 for a genomic-based model.</p><p><strong>Discussion: </strong>GWAS revealed the polygenic architecture of the resistance trait in the blue mussel. The genomic selection models studied showed overall better performance than the pedigree-based model in terms of accuracy of breeding values prediction. This work provides insights into the genetic basis of resistance to <i>V. splendidus</i> and exemplifies the potential of genomic selection in family-based breeding programs in <i>M. edulis</i>.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"15 ","pages":"1487807"},"PeriodicalIF":2.8,"publicationDate":"2025-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11739312/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143004035","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}