Genomics最新文献

{"title":"Methionine restriction reduced growth performance and exacerbated lipid deposition in hybrid grouper (Epinephelus fuscoguttatus ♀ × E. lanceolatus ♂) under high-lipid diets by suppressing the lipid degradation pathways with the single-cell RNA-seq analysis","authors":"Jiacheng Zhang ,&nbsp;Yinhuan Zhou ,&nbsp;Chunyan Liao ,&nbsp;Wenhao Gao ,&nbsp;Beiping Tan ,&nbsp;Shuyan Chi","doi":"10.1016/j.ygeno.2024.110960","DOIUrl":"10.1016/j.ygeno.2024.110960","url":null,"abstract":"<div><div>The experiment mainly focused on the liver of the hybrid grouper (<em>Epinephelus fuscoguttatus ♀ × E. lanceolatus ♂</em>) with low methionine levels by single-cell RNA-seq under high-lipid diets. Both weight gain rate (WGR) and specific growth rate (SGR) in the MR group were obviously lower than the C group<em>,</em> and the intraperitoneal fat (IPF) in the MR group was obviously enhanced than HL and C groups<em>,</em> which led to more visible growth inhibition and lipid deposition. By using the scRNA-seq analysis, nine cell types were classified as: liver parenchymal cells, erythrocytes, hepatic stellate cells, cholangiocytes, macrophages, T cells, epidermal cells, eosinophil and fibroblasts. Lipid and carbohydrate metabolisms were mainly enriched in liver parenchymal cells. The lipid degradation pathways were obviously inhibited in the MR group, such as cholesterol degradation pathway. The lipid degradation genes were obviously decreased in the MR group. In conclusion, methionine restriction might suppress the lipid degradation pathways in liver parenchymal cells, led to obvious lipid deposition.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"116 6","pages":"Article 110960"},"PeriodicalIF":3.4,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142618329","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":"Integrative analysis of whole genome bisulfite and transcriptome sequencing reveals the effect of sodium butyrate on DNA methylation in the differentiation of bovine skeletal muscle satellite cells","authors":"Xiaowei Wang ,&nbsp;Xiaonan Zhou ,&nbsp;Chenglong Li ,&nbsp;Chang Qu ,&nbsp;Yuangang Shi ,&nbsp;Cong-Jun Li ,&nbsp;Xiaolong Kang","doi":"10.1016/j.ygeno.2024.110959","DOIUrl":"10.1016/j.ygeno.2024.110959","url":null,"abstract":"<div><div>Butyric acid as a short-chain fatty acid (SCFA) is one of the key microbial metabolites of ruminants. Numerous studies indicate that butyrate is crucial in muscle growth and development, and plays an important molecular regulatory role mainly by inhibiting histone deacetylation. DNA methylation, a major epigenetic modification, is involved in cell differentiation. Butyrate, in addition to its role in acetylation modifications, can alter the DNA methylation status of cells. However, the impact of butyrate on the DNA methylation of bovine skeletal muscle satellite cells (SMSCs) remains unclear. In this study, we developed a differentiation model of SMSCs and employed RNA sequencing (RNA-seq) alongside whole genome bisulfite sequencing (WGBS) to explore the effects of butyrate treatment on DNA methylation status and its relationship with gene expression. Treatment of SMSCs with sodium butyrate (NaB) at 1.0 mM for 2 days significantly inhibited the expression of DNA methyltransferases (<em>DNMT1, DNMT2, DNMT3A</em>) at the mRNA and protein levels while promoting the expression of demethylases (<em>TET1, TET2, TET3</em>) at mRNA levels. WGBS identified 4292 differentially methylated regions (DMRs), comprising 2294 hypermethylated and 1998 hypomethylated regions. These DMRs were significantly enriched in the MAPK, cAMP, and Wnt signaling pathways, all of which are implicated in myogenesis and development. Combining RNA-seq and WGBS data revealed a total of 130 overlapping genes, including <em>MDFIC</em>, <em>CREBBP</em>, <em>DMD, LTBP2</em> and <em>KLF4</em>. These genes are predominantly involved in regulating the FoxO, MAPK, PI3K-Akt, and Wnt signaling pathways. This study provides new insights into the effects of butyrate-mediated DNA methylation on SMSC development and enhances our understanding of butyrate as an epigenetic modifier beyond its role in acetylation.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"116 6","pages":"Article 110959"},"PeriodicalIF":3.4,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142618328","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":"Melatonin promotes the proliferation of dermal papilla cells in cashmere goats via activation of chi-let-7d-5p/WNT2 axis","authors":"Junyang Liu ,&nbsp;Bin Liu ,&nbsp;Qing Mu ,&nbsp;Jiasen Liu ,&nbsp;Yunhua Li ,&nbsp;Wendian Gong ,&nbsp;Tergel Chahaer ,&nbsp;Yukun Song ,&nbsp;Erhan Hai ,&nbsp;Haoyuan Wang ,&nbsp;Yanjun Zhang ,&nbsp;Yanhong Zhao","doi":"10.1016/j.ygeno.2024.110961","DOIUrl":"10.1016/j.ygeno.2024.110961","url":null,"abstract":"<div><div>Exogenous melatonin promotes the differentiation of secondary hair follicles in Cashmere goats, thereby improving cashmere production. MicroRNAs (miRNAs) play a crucial role in regulating post-transcriptional gene expression and influence hair follicle growth. However, the mechanism through which melatonin regulates hair follicle development via miRNA mediation remains unclear. In this study, we used RNA-seq to identify differentially expressed (DE) miRNAs during melatonin-induced growth of secondary hair follicles in inner Mongolian Cashmere goats. In total, 170 DE miRNAs were identified. Enrichment analysis revealed that the target genes of these DE miRNAs were related to biological processes such as protein modification; cytoskeletal components; and the Notch, Wnt, and MAPK signaling pathways. The miRNA-mRNA regulatory network suggested that the DE miRNA chi-let-7d-5p negatively regulates <em>WNT2</em> expression. Mechanistic studies revealed that melatonin promotes the proliferation of DP cells in Cashmere goats via the chi-let-7d-5p/<em>WNT2</em> axis.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"116 6","pages":"Article 110961"},"PeriodicalIF":3.4,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142692858","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":"bta-miR-224 regulates milk fat metabolism by targeting FABP4 in bovine mammary epithelial cells","authors":"Chuanchuan Wang ,&nbsp;Jinyan Zhao ,&nbsp;Xiaofang Feng ,&nbsp;Wei Zhao ,&nbsp;Ruoshuang Ma ,&nbsp;Baojun Yu ,&nbsp;Lin Xue ,&nbsp;Hua Wang ,&nbsp;Yafei Chen ,&nbsp;Juan Zhang professor ,&nbsp;Yaling Gu","doi":"10.1016/j.ygeno.2024.110955","DOIUrl":"10.1016/j.ygeno.2024.110955","url":null,"abstract":"<div><div>Milk fat is produced and secreted by the mammary gland, which is mainly regulated by diet and gene-molecule network. Therefore, understanding the molecular mechanism of milk fat synthesis is of practical significance for improving milk quality. Fatty acid-binding protein 4 (<em>FABP4</em>) is a candidate messenger RNA (mRNA) closely linked to milk fat metabolism obtained from transcriptomic analysis of mammary epithelial cells of cows in the pre-existing high- and low-milk-fat groups, and its expression pattern and function are still unclear. The qRT-PCR results depicted that <em>FABP4</em> was highly expressed in bovine mammary epithelial cells (BMECs) in breast tissues and the high milk fat group. Subsequently, the regulatory effects of <em>FABP4</em> on BMECs were analyzed by CCK8, EdU, and flow cytometry, and the results demonstrated that <em>FABP4</em> inhibited the proliferation and viability of BMECs and promoted their apoptosis. Next, the effect of <em>FABP4</em> on milk lipid metabolism was explored. pEGFP-N1-FABP4 was transfected into BMECs, and <em>FABP4</em> upregulated the expression levels of the milk lipid marker genes <em>XDH</em>, <em>PPARG</em>, and <em>ACSS2</em>, and promoted the formation of triglycerides (TGs), cholesterol, lipid droplets, and β-casein. Strong interactions between FABP4 and PPARG were identified using STRING prediction. Western blotting revealed that FABP4 interacted with PPARG to promote PPARG expression, while the opposite result was observed after interfering with FABP4. The gene regulation of microRNA (miRNA) is essential for fatty acid metabolism and synthesis. Predicted by website and combined with pre-miRNA transcriptome sequencing results, we hypothesized that <em>FABP4</em> might be the target gene of bta-miR-224. The results of the dual-luciferase reporter gene and qRT-PCR revealed that bta-miR-224 negatively regulated <em>FABP4</em> expression by targeting the 3′-UTR of <em>FABP4</em>. By exploring the function of bta-miR-224, we observed that bta-miR-224 mimics downregulated the expression of the milk fat marker genes <em>AGPAT6</em>, <em>ACSS2</em>, and <em>XDH</em> and inhibited TG synthesis and lipid droplet secretion. However, the bta-miR-224 inhibitor depicted the opposite results. In conclusion, <em>FABP4</em> plays a crucial role in regulating BMEC proliferation and differentiation. Bta-miR-224 targeting <em>FABP4</em> may promote biological processes such as TG synthesis and lipid droplet formation through PPARG, which lays a solid foundation for further analysis of the functional mechanism of milk lipid metabolism in dairy cows from a miRNA-mRNA perspective.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"116 6","pages":"Article 110955"},"PeriodicalIF":3.4,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142557639","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":"A systematic benchmark of copy number variation detection tools for high density SNP genotyping arrays","authors":"M.N. van Baardwijk ,&nbsp;L.S.E.M. Heijnen ,&nbsp;H. Zhao ,&nbsp;M. Baudis ,&nbsp;A.P. Stubbs","doi":"10.1016/j.ygeno.2024.110962","DOIUrl":"10.1016/j.ygeno.2024.110962","url":null,"abstract":"<div><div>Copy Number Variations (CNVs) are crucial in various diseases, especially cancer, but detecting them accurately from SNP genotyping arrays remains challenging. Therefore, this study benchmarked five CNV detection tools—PennCNV, QuantiSNP, iPattern, EnsembleCNV, and R-GADA—using SNP array and WGS data from 2002 individuals of the DRAGEN re-analysis of the 1000 Genomes project. Results showed significant variability in tool performance. R-GADA had the highest recall but low precision, while PennCNV was the most reliable in terms of precision and F1 score. EnsembleCNV improved recall by combining multiple callers but increased false positives. Overall, current tools, including new methods, do not outperform PennCNV in precise CNV detection. Improved reference data and consensus on true positive CNV calls are necessary. This study provides valuable insights and scalable workflows for researchers selecting CNV detection methods in future studies.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"116 6","pages":"Article 110962"},"PeriodicalIF":3.4,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142638674","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":"Whole-Genome sequencing of Calonectria dianii: An important pathogen causing Eucalyptus leaf blight","authors":"QianLi Liu ,&nbsp;FeiFei Liu ,&nbsp;GuoQing Li ,&nbsp;KaiDong Liu ,&nbsp;ZhenChi Huang ,&nbsp;ShanNi Cao ,&nbsp;JunDi Zhong","doi":"10.1016/j.ygeno.2024.110967","DOIUrl":"10.1016/j.ygeno.2024.110967","url":null,"abstract":"<div><div>Eucalyptus leaf blight, caused by <em>Calonectria</em> spp., significantly impacts the global <em>Eucalyptus</em> industry. <em>Calonectria dianii</em>, as one of the predominant causal agents, poses a serious threat to <em>Eucalyptus</em> plantations in China. To enhance our understanding of its pathogenic mechanisms, we sequenced the genome of <em>C. dianii</em> RIFT 6520 using both Nanopore PromethION and Illumina NovaSeq PE150 platforms. Our analysis revealed a 61.76 Mb genome comprising 30 contigs with an N50 of 4,726,631 bp, a GC content of 49.74 %, and 10,184 predicted coding genes. Additionally, comparative genomic analysis between <em>C. dianii</em> and seven other significant plant-pathogenic <em>Calonectria</em> species was conducted. This analysis provided insights into the evolutionary relationships and adaptive mechanisms of these pathogens. Our study elucidates the genetic basis of <em>C. dianii's</em> pathogenicity and evolution, providing valuable information for future research on its molecular interactions with <em>Eucalyptus</em> and aiding in the development of precise control measures for Eucalyptus leaf blight.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"116 6","pages":"Article 110967"},"PeriodicalIF":3.4,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142692860","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":"Determining the effect of long non-coding RNA maternally expressed gene 3 (lncRNA MEG3) on the transcriptome profile in cervical cancer cell lines","authors":"Solomon Arega ,&nbsp;Suchanda Dey ,&nbsp;Sunil Pani ,&nbsp;Somya Ranjan Dash ,&nbsp;Roli Budhwar ,&nbsp;Chanakya Nath Kundu ,&nbsp;Niladri Ganguly","doi":"10.1016/j.ygeno.2024.110957","DOIUrl":"10.1016/j.ygeno.2024.110957","url":null,"abstract":"<div><div>This study investigates the role of the long non-coding RNA Maternally Expressed Gene3 (lncRNA MEG3) gene in cervical cancer, as evidenced by its downregulation in cancerous cell lines. The study demonstrates the effects of the overexpression of lncRNA MEG3 in cervical cancer cell lines, particularly in C33A and CaSki. Through comprehensive analyses, including Next-Generation Sequencing (NGS), alterations in global mRNA expression were analyzed. In C33A cells, 67 genes were upregulated, while 303 genes were downregulated. Similarly, in CaSki cells, 221 genes showed upregulation and 248 genes displayed downregulation. Gene ontology and KEGG pathway analyses were conducted to gain insight into potential mechanisms. Furthermore, the study delves into gene regulatory networks, uncovering intricate interactions among genes. The RNA sequencing data were confirmed for eight genes: PAX3, EGR2, ROR1, NRP1, OAS2, STRA6, CA9, and EDN2 by Real-time PCR. The findings illuminate the complex landscape of gene expression alterations and pathways impacted by the overexpression of lncRNA MEG3. The impact of MEG3 on the overall cervical cancer cells' mRNA profile is reported for the first time. New biomarkers for the prognosis of cervical cancer are also reported in this study. Moreover, identifying specific genes within the regulatory networks provides valuable insights into potential therapeutic targets for managing cervical cancer.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"116 6","pages":"Article 110957"},"PeriodicalIF":3.4,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142603976","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":"Regulation of cell-mediated immune responses in dairy bulls via long non-coding RNAs from submandibular lymph nodes, peripheral blood, and the spleen","authors":"Xiuxin Zhao ,&nbsp;Xiao Wang ,&nbsp;Guanghui Xue ,&nbsp;Yundong Gao ,&nbsp;Yuanpei Zhang ,&nbsp;Yanqin Li ,&nbsp;Yachun Wang ,&nbsp;Jianbin Li","doi":"10.1016/j.ygeno.2024.110958","DOIUrl":"10.1016/j.ygeno.2024.110958","url":null,"abstract":"<div><div>Cell-mediated immune responses (CMIRs) are critical to building a robust immune system and reducing disease susceptibility in cattle. Long non-coding RNAs (lncRNAs) regulate various biological processes. However, to the best of our knowledge, the characterization and functions of lncRNAs and their regulations on the bovine CMIR have not been investigated comprehensively. In this study, experimental bulls were immunized with heat-killed preparation of <em>Candida albicans</em> (HKCA) to induce delayed-type hypersensitivity (DTH). Three bulls were classified as high- CMIR responders and three were low-CMIR responders, based on their classical DTH skin reactions. LncRNAs were identified in the submandibular lymph nodes, peripheral blood, and spleen of high- and low-CMIR animals using strand-specific RNA sequencing. A total of 21,003 putative lncRNAs were identified across tissues, and 420, 468, and 599 lncRNAs were differentially expressed between the two groups in the submandibular lymph node, peripheral blood, and spleen tissues, respectively. Functional analysis of the differentially expressed lncRNA (DElncRNA) target genes showed that a number of immune-related Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were enriched, including immune response, cell adhesion, nucleosome, DNA packaging, antigen processing and presentation, and complement and coagulation cascades. Tissue specificity analysis indicated that lncRNA transcripts have stronger tissue specificity than mRNA. Furthermore, an interaction network was constructed based on DElncRNAs and DEGs, and 11, 14, and 11 promising lncRNAs were identified as potential candidate genes influencing immune response regulation in submandibular lymph nodes, peripheral blood, and spleen tissues, respectively. These results provide a foundation for further research into the biological functions of lncRNAs associated with bovine CMIR and identify candidate lncRNA markers for cell-mediated immune responses.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"116 6","pages":"Article 110958"},"PeriodicalIF":3.4,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142618326","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 evolution and patterns of horizontal gene transfer in Papilio","authors":"Jiajia Wang,&nbsp;Yunfei Wu,&nbsp;Linxin Zhu,&nbsp;Kaixin Guo,&nbsp;Shichen Gao,&nbsp;Yan Dong","doi":"10.1016/j.ygeno.2024.110956","DOIUrl":"10.1016/j.ygeno.2024.110956","url":null,"abstract":"<div><div>The Papilio genus, known for its ecological and phenotypic diversity, is a valuable model for evolutionary studies. This study conducted a comparative genomic analysis of 11 <em>Papilio</em> species, revealing species-specific gene family expansions, including the UDP-glucosyltransferase 2 gene associated with insect detoxification, particularly expanding in <em>Papilio polyxenes</em>. Our analysis also revealed 199 horizontal gene transfer (HGT) acquired genes from 76 microbial species, with <em>Pseudomonadota</em> and <em>Bacillota</em> as common HGT donors across these genomes. Furthermore, we examined the evolutionary patterns of nine ABC transporter subfamilies, uncovering potential links between gene family evolution and environmental adaptation. This study provides new insights into evolutionary relationships and genomic adaptations within the <em>Papilio</em> genus, contributing to broader butterfly evolutionary research.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"116 6","pages":"Article 110956"},"PeriodicalIF":3.4,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142618324","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 of heat stress-related genomic regions by genome-wide association study in Solanum tuberosum","authors":"Alexander Kaier ,&nbsp;Selina Beck ,&nbsp;Markus Ingold ,&nbsp;José María Corral ,&nbsp;Stephan Reinert,&nbsp;Uwe Sonnewald,&nbsp;Sophia Sonnewald","doi":"10.1016/j.ygeno.2024.110954","DOIUrl":"10.1016/j.ygeno.2024.110954","url":null,"abstract":"<div><div>The climate crisis impairs yield and quality of crucial crops like potatoes. We investigated the effects of heat stress on five morpho-physiological parameters in a diverse panel of 178 potato cultivars under glasshouse conditions. Overall, heat stress increased shoot elongation and green fresh weight, but reduced tuber yield, starch content and harvest index. Genomic information was obtained from 258 tetraploid and three diploid cultivars by a genotyping-by-sequencing approach using methylation-sensitive restriction enzymes. This resulted in an enrichment of sequences in gene-rich regions. Population structure analyses using genetic distances and hierarchical clustering revealed strong kinship but weak overall population structure cultivars. A genome-wide association study (GWAS) was conducted with a subset of 20 K stringently filtered SNPs to identify quantitative trait loci (QTL) linked to heat tolerance. We identified 67 QTL and established haploblock boundaries to narrow down the number of candidate genes. Additionally, GO-enrichment analyses provided insights into gene functions. Heritability and genomic prediction were conducted to assess the usability of the collected data for selecting breeding material. The detected QTL might be exploited in marker-assisted selection to develop heat-resilient potato cultivars.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"116 6","pages":"Article 110954"},"PeriodicalIF":3.4,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142544875","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}