BMC Genomics最新文献

{"title":"Characteristic analysis of N⁶-methyladenine in different parts of yak epididymis.","authors":"Ziqiang Ding, Xingdong Wang, Shaoke Guo, Yandong Kang, Mengli Cao, Liyan Hu, Ben Zhang, Lin Xiong, Jie Pei, Tao Yang, Xian Guo","doi":"10.1186/s12864-025-11684-w","DOIUrl":"10.1186/s12864-025-11684-w","url":null,"abstract":"<p><strong>Background: </strong>The epididymis is essential for sperm maturation. During sperm maturation, markable alterations of the payload of small noncoding RNAs are observed in the epididymis, which indicated the role of epigenetic alterations in sperm maturation. However, the N⁶-Methyladenosine (m⁶A) modification profile of the epididymis remains unelucidated. Therefore, in this study, we assessed the m⁶A modification levels in the caput, corpus, and cauda of the yak epididymis using a combination of methylated RNA immunoprecipitation and RNA sequencing.</p><p><strong>Results: </strong>The m⁶A levels were significantly increased in the corpus of the epididymis. Functional enrichment analysis of differentially methylated RNA (DMR) between the corpus and caput group revealed the significant enrichment of DMRs in the gap junction, ErbB signaling pathway, and mTOR signaling pathway, which participate in cell communication and sperm maturation. In addition, the DMRs of cauda-vs-corpus group were enriched in apoptosis, the FoxO signaling pathway, the PI3K-Akt signaling pathway, and the tumor necrosis factor signaling pathway that were associated with sperm autophagy, oxidative stress, and sperm maturation. Furthermore, we identified the key genes exhibiting significant changes in m⁶A levels but with no differences in RNA levels, including YY1-associated factor 2, forkhead box J2, and forkhead box O1. This finding indicated that m⁶A modifications affect these genes during translation, thereby participating in sperm maturation.</p><p><strong>Conclusions: </strong>In summary, we generated the m⁶A profile of the yak epididymis, which will aid in further elucidating the maturation process of sperm and reveal more information related to male infertility.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"500"},"PeriodicalIF":3.5,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12087211/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144101373","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":"Circ 0020938 inhibits hair follicle stem cells proliferation via the miR-142-5p/DSG4 axis in cashmere goats.","authors":"Jiamian Du, Menghua Sui, Zhihao Song, Shuangshuang Liang, Yujie Zheng, Xin Wang","doi":"10.1186/s12864-025-11642-6","DOIUrl":"10.1186/s12864-025-11642-6","url":null,"abstract":"<p><strong>Background: </strong>Shaanbei white cashmere goat is an excellent cashmere goat breed, and its market favored cashmere from the secondary hair follicles. Hair follicles mature around birth and each hair follicle repeatedly undergoes a growth cycle that comprises three distinct stages: anagen, catagen and telogen. Understanding the molecular mechanisms controlling cyclic hair follicle changes is essential for optimizing hair follicle function and improving cashmere production.</p><p><strong>Methods: </strong>The circRNA expression profile in the hair follicle cycle was constructed and differentially expressed circRNAs were identified, with particular focus on circ 0020938, which was highly expressed during anagen. The functional assays were performed to assess the effect of circ 0020938 on hair follicle stem cells (HFSCs) proliferation. Competing endogenous RNA (ceRNA) network was constructed to investigate the interaction between circ 0020938, miR-142-5p, and DSG4. Rescue experiment was conducted to validate the impact of circ 0020938 on HFSCs proliferation and DSG4 expression.</p><p><strong>Results: </strong>We found that circ 0020938 inhibited HFSCs proliferation. Further analysis revealed that circ 0020938 acted as a sponge for miR-142-5p, alleviating the repression of DSG4. Additionally, we confirmed that DSG4 inhibited HFSCs proliferation, suggesting that it play a key role in regulating the balance between proliferation and differentiation during the hair follicle cycle. Rescue experiments showed that the inhibition of HFSCs proliferation by circ 0020938 was partially reversed by miR-142-5p.</p><p><strong>Conclusion: </strong>Our study provides novel insights into the regulatory role of circRNA in HFSCs proliferation during the hair follicle cycle. The results demonstrate that circ 0020938 acts as a miRNA sponge and inhibits HFSCs proliferation through the miR-142-5p/DSG4 axis, thereby contributing to the proper progression of the hair follicle cycle.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"505"},"PeriodicalIF":3.5,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12090641/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144101376","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":"Biases from Oxford Nanopore library preparation kits and their effects on microbiome and genome analysis.","authors":"Ziming Chen, Chian Teng Ong, Loan To Nguyen, Harrison J Lamb, O González-Recio, M Gutiérrez-Rivas, Sarah J Meale, Elizabeth M Ross","doi":"10.1186/s12864-025-11649-z","DOIUrl":"10.1186/s12864-025-11649-z","url":null,"abstract":"<p><strong>Background: </strong>Oxford Nanopore sequencing is a long-read sequencing technology that does not rely on a polymerase to generate sequence data. Sequencing library preparation methods used in Oxford Nanopore sequencing rely on the addition of a motor protein bound to an adapter sequence, which is added either using ligation-based methods (ligation sequencing kit), or transposase-based methods (rapid sequencing kit). However, these methods have enzymatic steps that may be susceptible to motif bias, including the underrepresentation of adenine-thymine (AT) sequences due to ligation and biases from transposases. This study aimed to compare the recognition motif and relative interaction frequencies of these library preparation methods and assess their effects on relative sequencing coverage, microbiome, and methylation profiles. The impacts of DNA extraction kits and basecalling models on microbiome analysis were also investigated.</p><p><strong>Results: </strong>By using sequencing data generated by the ligation and rapid library kits, we identified the recognition motif (5'-TATGA-3') consistent with MuA transposase in the rapid kit and low frequencies of AT in the sequence terminus of the ligation kit. The rapid kit showed reduced yield in regions with 40-70% guanine-cytosine (GC) contents, while the ligation kit showed relatively even coverage distribution in areas with various GC contents. Due to longer reads, ligation kits showed increased taxonomic classification efficiency compared to the rapid protocols. Rumen microbial profile at different taxonomic levels and mock community profile showed significant variation due to the library preparation method used. The ligation kit outperformed the rapid kit in subsequent bacterial DNA methylation statistics, although there were no significant differences.</p><p><strong>Conclusions: </strong>Our findings indicated that careful and consistent library preparation method selection is essential for quantitative methods such as bovine-related microbiome analysis due to the systematic bias induced by the enzymatic reactions in Oxford Nanopore library preparation.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"504"},"PeriodicalIF":3.5,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12090612/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144101348","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative transcriptomics of transgenic tobacco plants overexpressing Miscanthus sinensis BTF3.","authors":"Ji Won Seo, Da Ye Ham, Jae Geun Lee, Hee Young Kim, Ik Young Choi, Myong Jo Kim, Eun Soo Seong","doi":"10.1186/s12864-025-11720-9","DOIUrl":"10.1186/s12864-025-11720-9","url":null,"abstract":"<p><strong>Background: </strong>Plant basic transcription factor3 (BTF3) plays an important role in photosynthesis rate and plant growth and development. In addition, it is involved in resistance mechanisms related to abiotic and biotic stress and has a significant impact on plant growth phenotype. This study was conducted to expand our understanding on plant transcriptome changes as there are no reports on plant transcriptome changes in normal environments due to the overexpression of Miscanthus sinensis BTF3 gene.</p><p><strong>Results: </strong>The amino acid sequence length of the BTF3 gene isolated from M. sinensis was 158 aa, and it showed the highest homology (97.47 %) with that of Paniocum virgatum (PvBTF3). Nicotiana benthamiana (Nb) transgenic plant was produced by transforming a binary vector into which the MsBTF3 gene was inserted into Agrobacterium. Up- and down-regulatory factors were classified through transcriptome analysis using transgenic plants overexpressing MsBTF3. Gene ontology (GO) analysis of up-regulated transcripts showed that the most expressed transcripts were involved in biological processes. Analysis of down-regulated differentially expressed genes (DEGs) showed that they were involved in metabolic processes that corresponded to biological processes. Blast analysis revealed that Nb03180T (chloroplast photosystem II 22 kDa component), Nb04871T (basic transcription factor 3-like), Nb13433T (expansin-B15- like), Nb15392T (receptor-like serine/threonine-protein kinase SD1-8 isoform X3), Nb17216T (3-bata-glucan endohydrolase), and Nb20214T (probable rhamnogalacturonate lyase B) were among the DEGs whose transcript expression was up-regulated more than 2-fold compared to the wild type. In particular, the reference gene, that is the NbBTF3 gene, showed the highest expression owing to the overexpression of MsBTF3.</p><p><strong>Conclusions: </strong>Transcriptome changes in tobacco plants through MsBTF3 overexpression revealed that MsBTF3 caused broad-spectrum changes in the biological processes of plants. MsBTF3 showed that various metabolic and defense responses could be activated by regulating the level of specific gene expression in plants. These data obtained through this process will greatly contribute to elucidating the mechanism by which MsBTF3 helps strong physiological responses in plants.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"506"},"PeriodicalIF":3.5,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12090582/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144101379","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":"Transcriptome sequencing of Antheraea pernyi antennae for identification of olfactory-related genes.","authors":"Xueting Liu, Shuwei Ma, Xinxue Zhang, Xue Li, Lei Nie, Guobao Wang","doi":"10.1186/s12864-025-11698-4","DOIUrl":"10.1186/s12864-025-11698-4","url":null,"abstract":"<p><strong>Background: </strong>In insects, the olfactory system governs physiological and behavioral processes by detecting various odorous molecules. Despite its economic importance and adaptability, the olfactory mechanism of Antheraea pernyi remains insufficiently understood, limiting its potential for pest management and as a model organism. Hence, we aimed to conduct transcriptome sequencing to explore olfactory-related genes in the antennae, serving as the most important olfactory organ in adult A. pernyi.</p><p><strong>Results: </strong>Based on the datasets, 1184 differently expressed genes (DEGs), including 484 upregulated and 700 downregulated genes, were identified by comparing the transcriptome profiles of the male and female antennae of A. pernyi. Moreover, 20, 7, 30, 11, and 2 candidate genes encoding odorant-binding proteins (OBPs), chemosensory proteins (CSPs), odorant receptors (ORs), ionotropic receptors (IRs), and sensory neuron membrane proteins (SNMPs), respectively, involved in pheromone perception, odor binding, pesticide resistance, and growth and development regulation were screened, and most of which were expressed in both male and female antennae while the expression levels of these candidate genes varied significantly between males and females. Multiple sequence alignment indicated that the six OBPs exhibited typical characteristics, containing six conserved Cys residues with the sequence of C1-X_26-30-C2-X₃-C3-X_41-42-C4-X_8-10-C5-X₈-C6. All CSPs followed a highly conserved pattern with four Cys residues arranged with an exact spacing of C1-X₆-C2-X_18-19-C3-X₂-C4. Different numbers of transmembrane domains were found in ORs, IRs, and SNMPs. In addition, several DEGs involve signal transduction underlying chemoreception were also identified from the transcriptome data, including guanine nucleotide-binding protein (G protein), cGMP-dependent protein kinase (PKA), calmodulin-A (CaM-A), mitogen-activated protein kinase 1 (MAPK1), and phospholipase D2 (PLD2).</p><p><strong>Conclusion: </strong>This study enriches the olfactory gene database of A. pernyi, providing insights into olfactory mechanisms crucial for mating and pest control, with implications for enhancing breeding strategies and ensuring the sustainability of the silk industry. These findings may serve as a theoretical foundation for a better understanding of the olfactory mechanisms of A. pernyi.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"499"},"PeriodicalIF":3.5,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12087209/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144092733","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":"Dynamic deployment of H2A.Z positive nucleosome mediated transcriptomic plasticity within vascular smooth muscle cell.","authors":"Chao Yu, Jiaxin Huang, Yan Wang, Jia Song, Wei Shen","doi":"10.1186/s12864-025-11679-7","DOIUrl":"10.1186/s12864-025-11679-7","url":null,"abstract":"<p><strong>Background: </strong>To maintain homeostasis in the mature human body, certain differentiated cells adopted high plasticity to refine their cellular functions. However, mechanisms that supported cellular plasticity still remained elusive. Here, through comprehensive transcriptomic and epigenetic studies of highly plastic vascular smooth muscle cells (SMCs), we aimed to decipher the chromatin basis that could mediate cellular plasticity.</p><p><strong>Results: </strong>In vascular smooth muscle cells, actively transcribed and highly adjustable genes tended to be associated with a continuously accessible region downstream of transcription start site (CAR-downTSS). This CAR-downTSS was located beyond the classic RNA polymerase II paused region, accessible at mono-nucleosome level and incorporated with histone variant H2A.Z. Depletion of H2A.Z reduced active histone modifications within CAR-downTSS, impaired RNA polymerase II transpassing when cells were stimulated, and consequently inhibited the ability of CAR-downTSS-associated genes to adjust their expression. Further in vitro and in vivo studies verified that this CAR-downTSS could be dynamically re-deployed onto different genes in vascular SMCs, whereas it was deployed in smaller quantities and remained quantitatively stable on genome within the quiescent cardiomyocytes.</p><p><strong>Conclusions: </strong>Vascular SMCs dynamically deployed H2A.Z-positive nucleosomes extending continuously downstream transcription start sites on different genes to support their transcriptional adjustability, which served as an important mechanism mediating cellular plasticity.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"502"},"PeriodicalIF":3.5,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12090464/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144101380","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":"The impact of GBSSI inactivation on starch structure and functionality in EMS-induced mutant lines of wheat.","authors":"Sujon Kumar, Yulong Li, Jia Zheng, Jing Liu, Qiang Xu, Yazhou Zhang, Huaping Tang, Pengfei Qi, Mei Deng, Jian Ma, Guoyue Chen, Yuming Wei, Youliang Zheng, Qiantao Jiang","doi":"10.1186/s12864-025-11630-w","DOIUrl":"10.1186/s12864-025-11630-w","url":null,"abstract":"<p><strong>Background: </strong>Starch, a major component of wheat (Triticum aestivum L.) grain, plays a crucial role in determining processing quality. Granule-bound starch synthase I (GBSSI), the enzyme primarily responsible for elongating α-1,4-glucan chains into linear amylose molecules, is a key determinant of starch quality. In this study, a mutant population of the wheat cultivar SM126, a high-quality variety form Sichuan, China, was generated using ethyl methanesulfonate (EMS) mutagenesis. This research investigates the effects of GBSSI inactivation on starch structure and functionality.</p><p><strong>Results: </strong>A waxy mutant (Wx-Abd) was identified by screening an M4 seed library with sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) of grain endosperm flour. DNA sequencing revealed a single nucleotide polymorphism (SNP) in the fourth exon, causing a premature stop codon and inactivation of the Wx-Abd allele. In previous work, the Wx-abD mutant was identified in the M2 generation, and crossing the M2-31 line with the M4-6165 line produced four distinct Wx protein subunits in the SM126 background. Comparisons between the Wx-abd line and the wild-type SM126 (Wx-AbD) showed significant differences in starch properties. The Wx-abd line exhibited reduced Wx gene expression, a distinct surface depression on starch granules, and a higher proportion of B-type starch granules. Notably, it exhibited significantly lower amylose content (7.02%) compared to SM126 (22.32%), along with a reduction in total starch content. Additionally, the Wx-abd line showed a higher gelatinization temperature.</p><p><strong>Conclusion: </strong>Inactivation of GBSSI in the Wx-abd line resulted in altered starch structure, particularly a decrease in amylose content and changes in granule morphology. These findings suggest that the Wx-abd line represents a valuable genetic resource for wheat breeding programs focused on improving starch quality for food production, with its high agronomic performance making it suitable for further breeding applications.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"501"},"PeriodicalIF":3.5,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12087110/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144101087","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":"Hybrid sequencing reveals the genome of a Chrysochromulina parva virus and highlight its distinct replication strategy.","authors":"Delaney Nash, Christine N Palermo, Ichiro Inamoto, Trevor C Charles, Jozef I Nissimov, Steven M Short","doi":"10.1186/s12864-025-11700-z","DOIUrl":"10.1186/s12864-025-11700-z","url":null,"abstract":"<p><p>Chrysochromulina parva (C. parva) is a eukaryotic freshwater haptophyte algae found in lakes and rivers worldwide. It is known to be infected by viruses, yet knowledge of the diversity and activity of these viruses is still very limited. Based on sequences of PCR-amplified DNA polymerase B (polB) gene fragments, Chrysochromulina parva virus BQ1 (CpV-BQ1) was the first known lytic agent of C. parva, and was considered a member of the virus family Phycodnaviridae, order Algavirales. However, the genome of a different C. parva-infecting virus (CpV-BQ2, or Tethysvirus ontarioense) from another virus family, the Mesomimiviridae, order Imitervirales, was the first sequenced. Here, we report the complete genome sequence of the putative phycodnavirus CpV-BQ1, accession PQ783904. The complete CpV-BQ1 genome sequence is 165,454 bp with a GC content of 32.32% and it encodes 193 open reading frames. Phylogenetic analyses of several virus hallmark genes including the polB, the late gene transcription factor (VLTF-3), and the putative A32-like virion packaging ATPase (Viral A32) all demonstrate that CpV-BQ1 is most closely related to other viruses in the phylum Megaviricetes within the order Algavirales, family Phycodnaviridae.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"498"},"PeriodicalIF":3.5,"publicationDate":"2025-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12085832/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144092727","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":"Population structure and mitogenomic analyses reveal dispersal routes of Macrobrachium nipponense in China.","authors":"Penghui Luo, Yiting Jin, Ting Zhao, Chao Bian, Zhimin Lv, Na Zhou, Jianguang Qin, Shengming Sun","doi":"10.1186/s12864-025-11692-w","DOIUrl":"10.1186/s12864-025-11692-w","url":null,"abstract":"<p><strong>Background: </strong>The oriental river prawn Macrobrachium nipponense is widely distributed in China, but its origin and distribution routes remain largely unknown. We collected 126 oriental river prawn specimens from four lakes and one river across China, and sequenced their mitochondrial cytochrome C oxidase subunit I (cox1) genes. We performed whole-genome resequencing of 100 samples and assembled mitogenomes for population analysis, these two types of mitochondrial markers (cox1 and all 13 protein-coding genes-13 PCGs), a nuclear marker (28S rRNA) and SNPs to infer the relationships between the five populations, the population structure, and migratory routes. We also assembled complete mitogenome per sampled population (5 in total) and used them to conduct comparative mitogenomic analyses.</p><p><strong>Results: </strong>The complete mitogenomes comprised 15,774-15,784 base pairs (bp). The average nucleotide diversity (π) of the populations, inferred using the cox1 gene data, was 0.03013 ± 0.00618, ranging from 0.00500 ± 0.00110 (Fuxian Lake) to 0.03562 ± 0.02538 (Khanka Lake). The identified haplotypes (33 cox1 and 101 13 PCGs) clustered into three main geographical lineages. Lineage A included Khanka Lake and one clade from the Haihe River. The specimens from Fuxian Lake constituted lineage B. Lineage C comprised a majority of specimens from the Haihe River, Taihu Lake, and Poyang Lake, and a minority of specimens from Khanka Lake and Fuxian Lake.</p><p><strong>Conclusions: </strong>This study indicates that native M. nipponense prawns in China originated from East China, subsequently spreading northward and westward into the inland regions along the Grand Canal and the Yangtze River system, forming distinct lineages. This proposed route improves our understanding of the geographic distribution and origin of M. nipponense in China.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"497"},"PeriodicalIF":3.5,"publicationDate":"2025-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12084929/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144092730","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 dissection of hundred-kernel weight through combined genome-wide association study and linkage analysis in tropical maize.","authors":"Mengfei Shi, Fuyan Jiang, Ranjan K Shaw, Babar Ijaz, Jiachen Sun, Xingming Fan","doi":"10.1186/s12864-025-11682-y","DOIUrl":"10.1186/s12864-025-11682-y","url":null,"abstract":"<p><strong>Background: </strong>Hundred-kernel weight (HKW) is a crucial determinant of maize yield. Understanding the genetic mechanisms underlying HKW is vital for maize breeding programs aimed at enhancing productivity. This study aimed to explore the genetic basis of HKW in maize using a multi-parent population (MPP), developed by crossing the common male parent Ye107 with five female parents representing a range of kernel sizes and weights. The MPP was evaluated under two distinct environmental conditions (19DH and 19BS).</p><p><strong>Results: </strong>Genotyping-by-sequencing (GBS) identified 591,483 high-quality single nucleotide polymorphisms (SNPs), which were used for a genome-wide association study (GWAS) and linkage analysis. The GWAS revealed 21 SNPs significantly associated with HKW, with Zm00001d028188, a gene involved in cell wall synthesis, emerging as a key candidate located on chromosome 1. This gene, encodes Galacturonosyltransferase 1 (GAUT1) and overlapped with two identified quantitative trait loci (QTLs): qHKW1-2 and qHKW1-3, which were further validated through linkage analysis.</p><p><strong>Conclusions: </strong>This study identified critical genetic loci and candidate genes, such as Zm00001d028188, involved in regulating HKW in maize. The findings provide valuable genomic resources for maize breeding, potentially contributing to the development of high-yielding maize varieties through an enhanced understanding of the genetic control of HKW.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"496"},"PeriodicalIF":3.5,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12085011/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144085544","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}