Genomics最新文献

{"title":"Transcriptome and metabolome reveal the mechanism of neuroendocrine regulation in ovarian development of broiler breeders","authors":"Xiaoli Zhou ,&nbsp;Yuhang Xu ,&nbsp;Cheng Fang ,&nbsp;Chutian Ye ,&nbsp;Weiming Liang ,&nbsp;Zhexia Fan ,&nbsp;Xuerong Ma ,&nbsp;Aijun Liu ,&nbsp;Xiquan Zhang ,&nbsp;Qingbin Luo","doi":"10.1016/j.ygeno.2025.111035","DOIUrl":"10.1016/j.ygeno.2025.111035","url":null,"abstract":"<div><div>The long-term selection for meat has led to the poor egg production efficiency in broiler. In this study, we analyzed the transcriptional levels of hypothalamus and ovary during the pre-laying (PP) and laying periods (LP) of broiler breeders. By combining these with the levels of reproductive hormones and ovarian metabolism, to reveal the neuroendocrine control mechanism of ovarian development. Results showed that during LP, the number of LYFs, SYFs and WFs, the thickness of the granular cell layer, and the serum LH, FSH, P4 and E2 levels were significantly increased (<em>P</em> &lt; 0.05). A total of 1188 and 2481 differentially expressed genes (DEGs) were detected in hypothalamus and ovary, respectively. 1972 significantly differentially metabolites (DMs) were detected in ovary. In hypothalamus, the expression of neuroendocrine regulatory genes such as <em>TRH</em>, <em>AVT</em>, <em>VIP</em>, and <em>NYB</em> in the Neuroactive ligand-receptor interaction pathway regulated the LH and FSH secretion via the HPG axis. In ovary, the promotion of GCs proliferation may occur through the glycerophospholipid metabolism pathway, which increased the thickness of the GCs layer. This helped to receive gonadotropin signals and increased P4 and E2 secretion. Meanwhile, the decreased expression levels of ovarian development inhibitory factors in the TGF-beta signaling pathway, including <em>BMP2</em>, <em>BMP4</em>, <em>BMP15</em> and <em>AMHR2</em>, and the increased expression levels of MMPs, including <em>MMP9</em>, <em>MMP11</em> and <em>MMP13</em>, may regulate the synthesis of metabolites associated with steroid hormone secretion and ovarian development, such as E2, E2-3S, 7α-OH-DHEA, CHO and AD. These genes and metabolites may play an important role in HPG axis in regulating ovarian development.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 3","pages":"Article 111035"},"PeriodicalIF":3.4,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143686521","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":"Integrated analysis of lipid metabolism and differentially expressed genes reveal seed oil accumulation in field muskmelon","authors":"Jiyuan Wang ,&nbsp;Hengyi Ren ,&nbsp;Jie Zhu ,&nbsp;Yahui Li ,&nbsp;Jie Liu ,&nbsp;Hu Li ,&nbsp;Chun Liu ,&nbsp;Yupeng Fan ,&nbsp;Huijun Zhang","doi":"10.1016/j.ygeno.2025.111031","DOIUrl":"10.1016/j.ygeno.2025.111031","url":null,"abstract":"<div><div>Field muskmelon (<em>Cucumis melo</em> L. var. <em>agrestis</em> Naud.), a novel oil crop, contains a high amount of lipids in seeds. However, the high-resolution profiles and dynamic regulation of its lipids remain largely unknown. This study identified the lipids and analyzed their dynamic changes using UHPLC-MS/MS. We identified 2533 lipid molecules in the seeds, including 7 categories and 47 sub-classes, with the higher proportions of glycerolipids (41.02 %) and glycerophospholipids (28.11 %). Moreover, the content of glycerolipids was the highest, particularly for triacylglycerol lipid molecules. Additionally, the expression patterns of differentially expressed genes (DEGs) showed a close correlation with lipid accumulation, especially within the plant hormone signaling pathway. Notably, the sufficient supply of 18:1-CoA, coupled with a high expression level of <em>CmFAD2</em>, contributed significantly to the high linoleic acid (68.56 %) content in field muskmelon seeds. Our findings offer insights that could enhance the comprehensive understanding of lipids in field muskmelon, and facilitate the breeding of field muskmelon.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 3","pages":"Article 111031"},"PeriodicalIF":3.4,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143673816","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":"Deep sequencing of Korean Jindo dog reveals evolutionary trajectory of coat color variations","authors":"Dayeon Kang ,&nbsp;Woncheoul Park ,&nbsp;Miju Kim ,&nbsp;Young-Jo Lim ,&nbsp;Jong-Seok Kim ,&nbsp;Seok-Il Oh ,&nbsp;Jocelyn Plassais ,&nbsp;Jaemin Kim ,&nbsp;Bong-Hwan Choi","doi":"10.1016/j.ygeno.2025.111032","DOIUrl":"10.1016/j.ygeno.2025.111032","url":null,"abstract":"<div><div>The inherent diversity of canines is closely intertwined with the unique color patterns of each dog population. These variations in color patterns are believed to have originated through mutations and selective breeding practices that occurred during and after the domestication of dogs from wolves. To address the significant gaps that persist in comprehending the evolutionary processes that underlie the development of these patterns, we generated and analyzed deep-sequenced genomes of 113 Korean Indigenous Jindo dogs that represent five distinct color patterns to identify the associated mutations in <em>CBD103</em>, <em>ASIP</em>, and <em>MC1R</em>. The degree of linkage disequilibrium and estimated allelic ages consistently indicate that the black-and-tan dogs descend from the first major founding population on Jindo island, compatible with the documented literature. We additionally demonstrate that black-and-tan dogs, in contrast to other color variations within the breed, exhibit a closer genetic affinity to ancient wolves from western Eurasia than those from eastern Eurasia. Lastly, the alleles unique to black-and-tan dogs indicated a pleiotropic effect by significantly decreasing the body size phenotypes compared to non-carriers. Overall, comparisons of whole genome sequences of each coat color population diverged from the same breed provided an unprecedented glimpse into the properties of evolutionary processes maintaining variation in Korean Jindo dog populations.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 3","pages":"Article 111032"},"PeriodicalIF":3.4,"publicationDate":"2025-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143656743","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":"METTL14 facilitates the process of sexual reversal via m6A RNA methylation in Pelodiscus sinensis","authors":"Tong Zhou ,&nbsp;Guobin Chen ,&nbsp;Jizeng Cao ,&nbsp;Huizi Ji ,&nbsp;Guiwei Zou ,&nbsp;Hongwei Liang","doi":"10.1016/j.ygeno.2025.111030","DOIUrl":"10.1016/j.ygeno.2025.111030","url":null,"abstract":"<div><div>The Chinese soft-shelled turtle (<em>Pelodiscus sinensis, P. sinensis</em>) demonstrates noteworthy sexual dimorphism, where the males grow more rapidly and significantly larger than females under equivalent conditions. Estradiol (E2) administration can catalyze transformation from male to pseudo-female (PF), during which m6A RNA methylation undergoes considerable alterations. Nevertheless, the function of m6A methylation, specifically, the methyltransferase 14, N6-adenosine-methyltransferase non-catalytic subunit gene (<em>METTL14</em>) during this sex reversal process remains unclear. Within this study, we characterized the <em>METTL14</em> gene, which was predominantly expressed within the ovary and demonstrated notable expression in PF individuals. Interference of <em>METTL14</em> results in altered expression of methylation-related genes, yielding elevated <em>RSPO1</em> expression and diminished <em>AMH</em> expression. Administration of E2 and <em>METTL14</em>-RNAi elicits 7994 differentially expressed genes (DEGs) during sexual differentiation, and KEGG enrichment analysis highlighted that <em>METTL14</em> profoundly affects embryonic development through pathways including steroid hormone biosynthesis, ovarian steroidogenesis, tryptophan metabolism, and Glycolysis/Gluconeogenesis. Gene set enrichment analysis (GSEA) indicated that METTL14-RNAi triggers reduced expression of steroid hormone biosynthesis and ovarian steroidogenesis pathways while increasing the PPAR signaling pathway. In conclusion, METTL14-RNAi results in significant up-regulation of <em>RSPO1</em> and down-regulation of <em>AMH</em>, inducing substantial alterations in pathways associated with hormone and metabolism. These findings propose that <em>METTL14</em> may play a facilitating role during E2-induced sex reversal in <em>P. sinensis</em>, offering a novel avenue for further exploration into all-male breeding.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 3","pages":"Article 111030"},"PeriodicalIF":3.4,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143624202","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":"Gap-free genome assembly and comparative analysis reveal the evolution and lignin degradation mechanisms of Cylindrobasidium torrendii","authors":"Yang Yang ,&nbsp;Jian Chen ,&nbsp;Xuebo Hu","doi":"10.1016/j.ygeno.2025.111029","DOIUrl":"10.1016/j.ygeno.2025.111029","url":null,"abstract":"<div><div>The Physalacriaceae family comprises numerous saprophytic edible and medicinal fungi with significant ecological and economic importance. However, the lack of high-quality genomic data has hindered systematic studies of this family. Here, we report the chromosome-level genome assembly of <em>Cylindrobasidium torrendii</em>, a species identified in China, using a combination of Illumina, PacBio HiFi, and Hi-C sequencing technologies. The 33.67 Mb genome, featuring a GC content of 52.00 %, demonstrates enhanced continuity and completeness. Phylogenetic analysis based on 1685 single-copy orthologous gene families places <em>C. torrendii</em> in close evolutionary proximity to <em>Armillaria mellea</em> and <em>Gymnopus necrorhizus</em>, with a divergence time of 112.39 Mya. Comparative genomics reveals conserved syntenic blocks between chromosomes of <em>C. torrendii</em> and those of <em>Pleurotus ostreatus</em> and <em>Lentinula edodes</em>. Gene family analysis identified 980 expanded and 487 contracted gene families, with expanded genes significantly enriched in secondary metabolite biosynthesis pathways. CAZyme, P450, and laccase gene family comparisons highlighted the evolutionary dynamics of these gene families in <em>C. torrendii</em>. Transcriptomic analysis under fungal dark stress revealed significant upregulation of genes such as <em>CtoLAC7</em> and CAZymes (<em>GH</em> and <em>CE</em> families). This study provides a high-quality genomic resource and novel insights into the genetic and functional characteristics of <em>C. torrendii</em> and the <em>Physalacriaceae</em> family.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 3","pages":"Article 111029"},"PeriodicalIF":3.4,"publicationDate":"2025-03-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143604483","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":"Integrated analysis of single-cell and bulk RNA sequencing identifies APOC1 as a biomarker and therapeutic target for G0/G1 cell cycle arrest in cholangiocarcinoma","authors":"Qinlei Wang ,&nbsp;Zhaowei Sun ,&nbsp;Maobing Wang ,&nbsp;Chuan Feng ,&nbsp;Menshou Chen ,&nbsp;Haoran Li ,&nbsp;Jingyun Guo ,&nbsp;Bingyuan Zhang ,&nbsp;Kai Ma ,&nbsp;Miao Liu ,&nbsp;Jinzhong Pang ,&nbsp;Yujie Feng","doi":"10.1016/j.ygeno.2025.111028","DOIUrl":"10.1016/j.ygeno.2025.111028","url":null,"abstract":"<div><div>Cholangiocarcinoma is characterized by its high malignancy, frequent recurrence and insensitivity to conventional radiotherapy and chemotherapy. This resistance may be associated with the presence of cells in the G0/G1 arrest phase within the cancer. Cancer cells in the G0/G1 phase are resistant to therapies targeting actively dividing cells, allowing them to evade conventional adjuvant treatments and survive. When conditions become favorable, these quiescent cells can re-enter the cell cycle, proliferate and potentially contribute to cancer recurrence. However, the biomarkers for identifying cells in the G0/G1 arrest phase within cholangiocarcinoma and the molecular mechanisms inducing G0/G1 arrest remain unclear. In our study, we first identified APOC1 as a characteristic gene for G0/G1 phase arrest in cholangiocarcinoma through bulk RNA sequencing (bulkRNA-seq). We then used single-cell RNA sequencing(scRNA-seq) for cell cycle inference and localized the expression peaks of APOC1 to verify its active cell cycle phase. Our experiments demonstrated that APOC1 can induce G0/G1 phase arrest in cholangiocarcinoma cells by inhibiting the Wnt/β-catenin signaling pathway, thereby suppressing cell proliferation, migration and invasion. This suggests that APOC1 may serve as a key regulatory factor and an important biomarker for cells in the G0/G1 phase of cholangiocarcinoma.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 3","pages":"Article 111028"},"PeriodicalIF":3.4,"publicationDate":"2025-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143596673","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 blacklist regions in cattle and pig genomes","authors":"Mei Kong ,&nbsp;Jingwen Dou ,&nbsp;Hong Liu ,&nbsp;Jing Xu ,&nbsp;Zhuqing Zheng ,&nbsp;Aishao Shangguan ,&nbsp;Zhenshuang Tang ,&nbsp;Xiaolong Qi ,&nbsp;Saixian Zhang ,&nbsp;Yue Xiang ,&nbsp;Yuhua Fu ,&nbsp;Xiaoyong Du ,&nbsp;Xinyun Li ,&nbsp;Liangliang Fu ,&nbsp;Zhonglin Tang ,&nbsp;Jingjin Li","doi":"10.1016/j.ygeno.2025.111027","DOIUrl":"10.1016/j.ygeno.2025.111027","url":null,"abstract":"<div><div>Cattle and pigs are important farm animals and biomedical models for studying human development and diseases. Accurate annotation of their cis-regulatory elements is essential for advancing breeding strategies and biological research. Identifying these elements typically relies on ChIP-seq data, which profiles histone modifications and transcription factors. Although some large-scale ChIP-seq projects have decoded functional genomes in cattle and pigs, no comprehensive blacklist identification has been performed. In this study, we systematically identified and evaluated blacklist regions in cattle and pig genomes using the ENCODE pipeline. We annotated 126.8 Mb and 99.9 Mb of blacklist regions in cattle and pigs, respectively. We found that removing these blacklist regions is a critical quality control measure that can enhance the reliability of ChIP-seq analysis. Overall, our results provide a valuable resource for farm animal research, and we propose eliminating these problematic regions to reduce abnormally high signals and improve downstream analyses.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 3","pages":"Article 111027"},"PeriodicalIF":3.4,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143580538","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":"Comprehensive expression genome-wide association study of long non-coding RNAs in four porcine tissues","authors":"Liyan Deng ,&nbsp;Marta Gòdia ,&nbsp;Martijn F.L. Derks ,&nbsp;Barbara Harlizius ,&nbsp;Samin Farhangi ,&nbsp;Zhonglin Tang ,&nbsp;Martien A.M. Groenen ,&nbsp;Ole Madsen","doi":"10.1016/j.ygeno.2025.111026","DOIUrl":"10.1016/j.ygeno.2025.111026","url":null,"abstract":"<div><h3>Background</h3><div>Long non-coding RNAs (lncRNAs), a type of non-coding RNA molecules, are known to play critical regulatory roles in various biological processes. However, the functions of the majority of lncRNAs remain largely unknown, and little is understood about the regulation of lncRNA expression. In this study, high-throughput DNA genotyping and RNA sequencing were applied to investigate genomic regions associated with lncRNA expression, commonly referred to as lncRNA expression quantitative trait loci (eQTLs). We analyzed the liver, lung, spleen, and muscle transcriptomes of 100 three-way crossbred sows to identify lncRNA transcripts, explore genomic regions that might influence lncRNA expression, and identify potential regulators interacting with these regions.</div></div><div><h3>Result</h3><div>We identified 6380 lncRNA transcripts and 3733 lncRNA genes. Correlation tests between the expression of lncRNAs and protein-coding genes were performed. Subsequently, functional enrichment analyses were carried out on protein-coding genes highly correlated with lncRNAs. Our correlation results of these protein-coding genes uncovered terms that are related to tissue specific functions. Additionally, heatmaps of lncRNAs and protein-coding genes at different correlation levels revealed several distinct clusters. An expression genome-wide association study (eGWAS) was conducted using 535,896 genotypes and 1829, 1944, 2089, and 2074 expressed lncRNA genes for liver, spleen, lung, and muscle, respectively. This analysis identified 520,562 significant associations and 6654, 4525, 4842, and 7125 eQTLs for the respective tissues. Only a small portion of these eQTLs were classified as cis-eQTLs. Fifteen regions with the highest eQTL density were selected as eGWAS hotspots and potential mechanisms of lncRNA regulation in these hotspots were explored. However, we did not identify any interactions between the transcription factors or miRNAs in the hotspots and the lncRNAs, nor did we observe a significant enrichment of regulatory elements in these hotspots. While we could not pinpoint the key factors regulating lncRNA expression, our results suggest that the regulation of lncRNAs involves more complex mechanisms.</div></div><div><h3>Conclusion</h3><div>Our findings provide insights into several features and potential functions of lncRNAs in various tissues. However, the mechanisms by which lncRNA eQTLs regulate lncRNA expression remain unclear. Further research is needed to explore the regulation of lncRNA expression and the mechanisms underlying lncRNA interactions with small molecules and regulatory proteins.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 3","pages":"Article 111026"},"PeriodicalIF":3.4,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143572693","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":"16S rDNA sequencing reveal synergistic effects of silkworm feces and earthworms on nutrient-poor soil microbial community structure and function in Guangxi","authors":"Fuzhi Lu ,&nbsp;Jinmei Wei ,&nbsp;Delong Guan ,&nbsp;Yuhan Peng ,&nbsp;Jing Song ,&nbsp;Feng Qian","doi":"10.1016/j.ygeno.2025.111025","DOIUrl":"10.1016/j.ygeno.2025.111025","url":null,"abstract":"<div><div>This study evaluates the synergistic effects of silkworm feces and earthworms on nutrient-poor acidic red soils in Guangxi, China. Using 16S rDNA amplicon sequencing, soil samples from untreated fields, silkworm feces, earthworm gut contents, and soils treated with silkworm feces combined with three earthworm densities (50, 80, and 110 worms/kg) were compared. The earthworm gut microbiome increased in diversity in a density-dependent manner, while treated soils displayed enhanced microbial richness—with the 80 worms/kg treatment showing the highest diversity (605 genera). Random Forest analysis identified key bacterial genera, and co-occurrence networks pinpointed potential keystone taxa. PICRUSt2 predicted enrichment of pathways for xenobiotic biodegradation, carbohydrate metabolism, and secondary metabolite biosynthesis. These findings demonstrate that integrating silkworm feces with an optimal earthworm density improves soil microbial diversity and function, offering insights for sustainable organic waste management and soil health.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 3","pages":"Article 111025"},"PeriodicalIF":3.4,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143566820","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":"Genetic variation underlying nitrogen-deficiency tolerance in Gossypium hirsutum during the seedling stage","authors":"Xing Lv ,&nbsp;Yuxin Song ,&nbsp;Huifeng Ke,&nbsp;Zhengwen Sun,&nbsp;Yan Zhang,&nbsp;Xingfen Wang,&nbsp;Zhiying Ma,&nbsp;Qishen Gu","doi":"10.1016/j.ygeno.2025.111019","DOIUrl":"10.1016/j.ygeno.2025.111019","url":null,"abstract":"<div><div>As over-fertilization leads to environmental concerns, selecting high yield cotton cultivars with a high nitrogen use efficiency (NUE) has become crucially important. However, the genetic effects underlying NUE traits remain unclear. In this study, a genome-wide association study (GWAS) was performed using 2.65 million high-quality single-nucleotide polymorphisms (SNPs) based on three NUE related traits at the seedling stage of 419 core accessions in four environments. A total of 21 novel loci were detected, of which, the novel peak on D10 chromosome was consistently detected for multiple traits and selected to analyze. We further identified and validated a novel candidate gene <em>GhERF4</em> by RNA-seq, RT-qPCR, virus-induced gene silencing (VIGS) and overexpression methods, and the results suggest that <em>GhERF4</em> plays a negative role in the regulation of N-deficiency tolerance. The identified SNPs and candidate genes provide new insights into understanding the molecular mechanism and breeding varieties in N-efficient tolerance.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 111019"},"PeriodicalIF":3.4,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143500282","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}