BMC Genomics最新文献

{"title":"Genome-wide association mapping for heat shock tolerance in Mercenaria mercenaria through SNP microarray analysis.","authors":"Huiping Yang, Denis Grouzdev, Zhenwei Wang, Jayme C Yee, Yangqing Zeng, Leslie Sturmer, Bassem Allam","doi":"10.1186/s12864-025-11689-5","DOIUrl":"10.1186/s12864-025-11689-5","url":null,"abstract":"<p><strong>Background: </strong>The northern quahog Mercenaria mercenaria is a major aquaculture species on the US East Coast, and heat resistance is the most sought trait for aquaculture. This study aimed to establish a genome-wide association for heat tolerance using a 66K SNP array for M. mercenaria. Quahogs from three farms were combined for a heat challenge at 1 °C per day from 24 °C to 35 °C and stay for two days (Phase I), decreasing to 27 °C in 24 h, to 24 °C in another 24 h, and maintaining at 24 °C (Phase II) until no one dead within 48 h at 24 °C (Phase III). Dead and live quahogs were sampled for genotyping using the SNP array.</p><p><strong>Results: </strong>During the heat challenge, different mortalities among the quahogs from the three farms were identified at 38, 46, and 55% at Phase I, and 36, 30, and 29% at Phase II. For the survivors (Phase III), no changes were found in body weight before and after the heat shock challenges (p < 0.265). The PCA analyses of SNP frequencies indicated significant genetic differences associated with quahog survival under heat stress across the different farms. The heritability of the heat tolerance was 0.680 ± 0.063. GWAS analysis indicated that one SNP exhibited a significant association with the time-to-death trait on chromosome 7 (p = 1.98 × 10^- 5). More significant SNPs (p < 10^- 3.5) were inside genes that have been reported to function in heat tolerance such as serine/threonine-protein kinase 31 and carbohydrate sulfotransferase 11, and some genes found within 50 K bp far from SNP sites have a relationship with heat tolerance such as toll-like receptors 4 and 6 (TLRs 4 and TLRs 6), uracil-DNA glycosylase, and a disintegrin and metalloproteinase with thrombospondin motifs gon-1 (ADAMTs).</p><p><strong>Conclusion: </strong>The fastStructure analysis revealed the proportions of different ancestral components within the quahogs from different farming stocks, highlighting that the genetic factors may contribute to their varying survival rates under heat stress. The associated genes have potential roles in immune response, cellular stress, and tissue repair. The findings highlighted the power of high-throughput approaches for the identification of superior quahog genotypes for further breeding.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"547"},"PeriodicalIF":3.5,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12123719/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144186408","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":"Genome-wide analysis of the Tritipyrum bHLH gene family and the response of TtbHLH310 in salt-tolerance.","authors":"Kuiyin Li, Chunlei Cong, Yingjian Wang, Hailing Zhang, Yong Li, Jie Xiao, Yanqing Ding, Lai Zhang","doi":"10.1186/s12864-025-11657-z","DOIUrl":"10.1186/s12864-025-11657-z","url":null,"abstract":"<p><strong>Background: </strong>The bHLH transcription factor is prevalent across the plant kingdom and is crucial for various abiotic stress responses in different plant species. Tritipyrum, an octoploid created from an intergeneric cross between Triticum aestivum (AABBDD) and Thinopyrum elongatum (EE), serves as a significant source of germplasm, facilitating the incorporation of desirable traits from Th. elongatum into T. aestivum. With the recent availability of the complete genome sequences of T. aestivum and Th. elongatum, it has become feasible to investigate the organization and expression patterns of bHLH genes within the Tritipyrum genome.</p><p><strong>Results: </strong>In this study, a total of 398 bHLH genes (TtbHLH) were identified within the Tritipyrum genome. These genes were classified into twenty major groups based on evolutionary analysis, indicating that they share conserved motif compositions. The TtbHLH genes are distributed across 28 chromosomes and include 67 duplication events. Synteny analysis suggests a common ancestral lineage for the bHLH gene family. Transcriptome data and quantitative polymerase chain reaction (qPCR) expression profiling identified 29 TtbHLH genes with significantly elevated expression levels in response to various salt-stress conditions and recovery treatments. Notably, Tel1E01T336100 (TtbHLH310) demonstrated a pronounced sensitivity to salt stress and is phylogenetically related to the salt-tolerant gene AtbHLH6 in Arabidopsis thaliana. Additionally, Pearson correlation analysis revealed 485 genes that exhibited a strong positive correlation (R > 0.9) with TtbHLH310 expression, which was enriched in pathways related to metabolic activities, cellular processes, stimulus responses, and biological regulation. Further analysis through real-time PCR confirmed that TtbHLH310 is highly expressed in the roots, stems, and leaves under salt-stress conditions.</p><p><strong>Conclusions: </strong>The findings indicate that TtbHLH310 may play a pivotal role in enhancing salt stress tolerance in plants. Its strong expression in response to salt stress highlights its potential as a valuable foreign gene for improving salt tolerance in wheat. These insights contribute to our understanding of the molecular mechanisms underpinning abiotic stress responses in Tritipyrum and may aid in the development of more resilient wheat varieties.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"549"},"PeriodicalIF":3.5,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12123985/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144186407","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":"Combining a novel ensemble model and multiplex methylation SNaPshot assays for saliva age prediction and cross-platform data analysis.","authors":"Benyang Xiao, Yuxiang Zhou, Zhirui Zhang, Xindi Wang, Jiali Xiang, Zhixin Lv, Miao Liao, Haibo Luo, Feng Song","doi":"10.1186/s12864-025-11713-8","DOIUrl":"10.1186/s12864-025-11713-8","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"546"},"PeriodicalIF":3.5,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12124079/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144186405","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":"Decoding the chloroplast genomes of five Iranian Salvia species: insights into genomic structure, phylogenetic relationships, and molecular marker development.","authors":"Amir Mohammad Akrami, Sepehr Meratian Esfahani, Aboozar Soorni","doi":"10.1186/s12864-025-11729-0","DOIUrl":"10.1186/s12864-025-11729-0","url":null,"abstract":"<p><strong>Background: </strong>The genus Salvia, a prominent member of the Lamiaceae family, is renowned for its ecological, medicinal, and economic significance. Despite its importance, molecular data, particularly chloroplast (cp.) genome information, remain scarce for many native Iranian Salvia species. In this study, we sequenced and analyzed the complete cp. genomes of five Iranian Salvia species (S. aethiopis, S. sclarea, S. glutinosa, S. verticillata, and S. officinalis) to elucidate their genomic structure, evolutionary relationships, and potential for biotechnological applications.</p><p><strong>Results: </strong>The cp. genomes of the five Salvia species exhibited a conserved quadripartite structure, with sizes ranging from 151,163 to 151,662 bp, and a GC content of 38%. Each genome contained 132 or 131 genes, comprising 86 or 87 protein-coding, 8 rRNA, and 37 tRNA genes, with duplications in rpl2, rpl23, and rps12. Minor variations in gene content were observed, such as the absence of trnS-CGA in S. glutinosa. Comparative analysis of IR boundaries showed subtle expansions in S. officinalis and S. sclarea, while S. glutinosa remained stable. Trans-splicing of the rps12 gene was observed in all species, with complex structures in S. glutinosa and S. sclarea. Codon usage analysis revealed a preference for A/U-ending codons, with S. verticillata displaying unique patterns. Nucleotide diversity (Pi) identified highly variable regions, such as rpl14-rpl16 and psbK-psbI, as potential molecular markers. Phylogenetic analysis resolved distinct clades, with S. aethiopis and S. sclarea forming a close group, S. glutinosa clustering with S. chanryoenica, and S. officinalis showing genetic homogeneity with Mediterranean species. S. verticillata exhibited an earlier divergence, highlighting the genus's evolutionary complexity.</p><p><strong>Conclusions: </strong>This study provides critical genomic resources for species identification, phylogenetic studies, and the development of molecular markers, facilitating the conservation of native Salvia species and their utilization in breeding programs for medicinal and aromatic traits.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"545"},"PeriodicalIF":3.5,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12123993/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144186406","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":"Minimal repeats are ubiquitous sites of crossover and recombination across the human genome.","authors":"Mina Ohadi, Nahid Tajeddin, Hadi Bayat, Dale J Annear, Ali M A Maddi, Hamid R Khorram Khorshid, Kaveh Kavousi, Ahmad Delbari, Alireza Nikkhah, Masoud Arabfard","doi":"10.1186/s12864-025-11734-3","DOIUrl":"10.1186/s12864-025-11734-3","url":null,"abstract":"<p><strong>Background: </strong>Crossover and recombination create genetic diversity that reflects differences in the DNA sequences of different organisms. We previously reported that trinucleotide 2-repeat units (T2Us) are sites of crossover and consequent colonization, which are massively spread and shared across the genomes of human and several other primates. These sites underscore the preference for AT- over CG-rich sequences as recombination sites.</p><p><strong>Methods: </strong>We extended our study to simpler repeat cores, consisting of AT/TA and CG/GC dinucleotides. An algorithm was designed to extract the genomic regions with a higher probability of recombination. To this end, we hypothesized that dinucleotide 3-repeat units (D3Us) are, at least in part, the basic overlapping units resulting from unequal crossover between dinucleotide 2-repeat units (D2Us). We mapped TATATA, ATATAT, CGCGCG, and GCGCGC across the human genome and analyzed their colonization (the distance between consecutive D3Us < 500 bp). We also studied several randomly selected colonies of diverse sizes in up to 100 vertebrate species using the UCSC and Ensembl Genome Browsers.</p><p><strong>Results: </strong>We found approximately four million AT/TA D3Us and one hundred thousand CG/GC D3Us across the human genome. The majority of these D3Us resided in colonies and spread ubiquitously along all chromosomes. AT/TA colonies were significantly larger and more intricate than CG/GC colonies. D2Us and D3Us were the primary sites of unequal crossover in these colonies, resulting in the emergence of primary recombinants (overlapping recombinants of D2Us/D3Us) and a vast repertoire of secondary recombinants (non-overlapping recombinants of D2Us/D3Us) and eventually, colonies of enormous intricacy and significance based on Poisson distribution. Intricacy was consistently detected across diverse colony sizes, from the smallest to the largest. The randomly selected colonies that were studied in other species were specific to or of their largest size in human.</p><p><strong>Conclusion: </strong>We report ubiquitous and intricate colonies, in which D2Us and D3Us were the primary sites of crossover and recombination. It is plausible that minimal repeats such as D2Us, D3Us, and T2Us mark recombination as a ubiquitous rule across the human genome. This phenomenon is likely to transform our understanding of the magnitude, biological, and evolutionary outcomes of crossover and recombination.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"550"},"PeriodicalIF":3.5,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12124074/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144186473","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":"De novo assembly of plasmodium interspersed repeat (pir) genes from Plasmodium vivax RNAseq data suggests geographic conservation of sub-family transcription.","authors":"Timothy S Little, Deirdre A Cunningham, George K Christophides, Adam James Reid, Jean Langhorne","doi":"10.1186/s12864-025-11752-1","DOIUrl":"10.1186/s12864-025-11752-1","url":null,"abstract":"<p><strong>Background: </strong>The plasmodium interspersed repeats (pir) multigene family is found across malaria parasite genomes, first discovered in the human-infecting species Plasmodium vivax, where they were initially named the virs. Their function remains unknown, although studies have suggested a role in virulence of the asexual blood stages. Sub-families of the P. vivax pir/virs have been identified, and are found in isolates from across the world, however their transcription at different localities and in different stages of the life cycle have not been quantified. Multiple transcriptomic studies of the parasite have been conducted, but many map the pir reads to existing reference genomes (as part of standard bioinformatic practice), which may miss members of the multigene family due to its inherent variability. This obscures our understanding of how the pir sub-families in P. vivax may be contributing to human/vector infection.</p><p><strong>Results: </strong>To overcome the issue of hidden pir diversity from utilising a reference genome, we employed de novo transcriptome assembly to construct the pir 'reference' of different parasite isolates from published and novel RNAseq datasets. For this purpose, a pipeline was written in Nextflow, and first tested on data from the rodent-infecting P. c. chabaudi parasite to ascertain its efficacy on a sample with a full, genome-based set of pir gene sequences. The pipeline assembled hundreds of pirs from the studies included. By performing BLAST sequence identity comparisons with reference genome pirs (including P. vivax and related species) we found a clustered network of transcripts which corresponded well with prior sub-family annotations, albeit requiring some updated nomenclature. Mapping the RNAseq datasets to the de novo transcriptome references revealed that the transcription of these updated pir gene sub-families is generally consistent across the different geographical regions. From this transcriptional quantification, a time course of mosquito bloodmeals (after feeding on an infected patient) highlighted the first evidence of ookinete stage pir transcription in a human-infective malaria parasite.</p><p><strong>Conclusions: </strong>De novo transcriptome assembly is a valuable tool for understanding highly variable multigene families from Plasmodium spp., and with pipeline software these can be applied more easily and at scale. Despite a global distribution, P. vivax has a conserved pir sub-family structure-both in terms of genome copy number and transcription. We suggest that this indicates important roles of the distinct sub-families, or a genetic mechanism maintaining their preservation. Furthermore, a burst of pir transcription in the mosquito stages of development is the first glint of ookinete pir expression for a human-infective malaria parasite, suggesting a role for the gene family at a new stage of the lifecycle.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"544"},"PeriodicalIF":3.5,"publicationDate":"2025-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12121038/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144179594","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":"Characterizing age-related features for assessing biological age and characteristics in Xinjiang Brown cattle.","authors":"Jiahao Wang, Menghua Zhang, Qingyao Zhao, Siqian Chen, Yongjie Tang, Quanzhen Chen, Lei Xu, Dan Wang, Xiaoping Guo, Kai Xing, Yachun Wang, ChuduanWang, Xixia Huang, Ying Yu","doi":"10.1186/s12864-025-11430-2","DOIUrl":"10.1186/s12864-025-11430-2","url":null,"abstract":"<p><strong>Background: </strong>Productive lifespan is a critical economic trait for both dual-purpose and dairy cows, as it determines lifetime milk production. Xinjiang Brown cattle, a dual-purpose breed widely raised in China's Xinjiang region, have a population of nearly two million and play a vital role in the local economy. However, the molecular mechanisms influencing aging and productive lifespan in Xinjiang Brown cattle remain largely unknown. In this study, we collected white blood cell (leukocyte) transcriptome data from 66 Xinjiang Brown cattle, aged 31 to 160 months, to investigate the dynamic changes in their gene expression profiles across different ages and identify genes potentially influencing their aging process.</p><p><strong>Results: </strong>A total of 1140 genes were identified as exhibiting a linear change in expression with age, while 697 genes showed non-linear changes, mainly enriched in immune and disease-related pathways. Linear genes were selected using elastic network regression to construct a transcriptomic clock and estimate the biological age of each sample. Individuals with older biological ages trend to highly express aging-related genes such as S100A8, while individuals with younger biological ages will highly express anti-aging genes such as BLVRB. We identified PGA5, LOC789748, ENSBTAG00000048555, and ENSBTAG00000050566 as crucial targets for anti-aging interventions, which exhibit reduced expression in biologically younger individuals and increased expression in biologically older ones. Performing sliding window analysis on non-linear genes, we elucidated changes in the expression of candidate genes at the age of 67 months, which are predominantly associated with endocrine pathways, such as GnRH and insulin secretion.</p><p><strong>Conclusions: </strong>This study characterized the age-related gene expression changes in Xinjiang Brown cattle and developed a transcriptomic clock specifically for calculating their biological age. It provides a valuable tool for assessing the aging status of Xinjiang Brown cattle and identifies key genes that may influence their aging process.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"542"},"PeriodicalIF":3.5,"publicationDate":"2025-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12121290/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144179799","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":"Transcriptomic and proteomic studies of body size and carcass traits and the longest dorsal muscle in Tibetan sheep.","authors":"Dehui Liu, Xue Li, Lei Wang, Quanbang Pei, Jincai Zhao, De Sun, Qianben Ren, Buying Han, Hanjing Jiang, Wenkui Zhang, Rong Li, Guoxiang Bao, Song Wang, Fei Tian, Sijia Liu, Kai Zhao, Dehong Tian","doi":"10.1186/s12864-025-11738-z","DOIUrl":"10.1186/s12864-025-11738-z","url":null,"abstract":"<p><strong>Background: </strong>Tibetan sheep represent valuable genetic resources on the Tibetan Plateau, and their body size and carcass traits serve as crucial foundations for breeding program development and breeding effects evaluation. The study of body size and carcass characteristics of Tibetan sheep helps to understand their process of genetic regulation.</p><p><strong>Result: </strong>The body size traits, carcass traits, and muscle fiber structure of plateau-type Tibetan and Zhashijia sheep were compared. Zhashijia ewes displayed considerably higher carcass weight and body size than plateau-type ewes. Additionally, it was observed that Zhashijia rams exhibited significantly greater eye muscle area, chest width, and muscle fiber perimeter in comparison to plateau-type rams. And Glycogen staining results showed that the glycogen content of the plateau-type Tibetan sheep was significantly higher than that of the Zhashijia sheep. Through transcriptomic and proteomic analyses, we identified 366 genes that showed differential expression in the ram group and 248 proteins with differential expression. In the ewe group, we found 623 differentially expressed genes (DEGs) and 624 differentially expressed proteins (DEPs). Among these, eleven genes and fourteen proteins were associated with body size and carcass quality. These genes and proteins showed significant enrichment in the PPAR signaling pathway and protein digestion and absorption. Furthermore, employing weighted gene co-expression network analysis (WGCNA) allowed us to identify twelve genes that are pivotal in regulating body size and carcass. Finally, RT-qPCR validation confirmed the reliability of our RNA-Seq results.</p><p><strong>Conclusion: </strong>The findings of this study contribute to a deeper comprehension of the morphological characteristics and carcass traits of Tibetan sheep, thereby establishing a robust scientific basis for the selective breeding of novel sheep breeds with enhanced growth performance and superior meat production capacity.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"543"},"PeriodicalIF":3.5,"publicationDate":"2025-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12121134/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144180472","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 tritrophic plant-insect-pathogen system used to develop a closely linked Rag2 and Rsv1-h recombinant haplotype in double-resistant soybean germplasm.","authors":"Luis G Posadas, Edson Ll Baldin, Lia Marchi-Werle, Tiffany M Heng-Moss, Scott Speck, Robert M Stupar, Kent M Eskridge, George L Graef","doi":"10.1186/s12864-025-11686-8","DOIUrl":"10.1186/s12864-025-11686-8","url":null,"abstract":"&lt;p&gt;&lt;strong&gt;Background: &lt;/strong&gt;The colocalization of two resistance (R) genes on chromosome 13 of soybean (Glycine max (L.) Merrill) that confer resistance against the soybean aphid (Aphis glycines) and soybean mosaic virus (SMV) gives rise to a very unique R-avr tritrophic incompatible interaction system that goes across biological kingdoms. In this tritrophic system, the insect is the only natural vector of the virus and soybean is a host-plant for both pests/pathogen. The almost unavoidable co-evolution of pathogen-vector with that of the R-genes in soybean plants through an endless arms race to avoid each other's defense-attack mechanisms raises interesting questions. The objectives of this work were to (i) develop double-resistant recombinant inbred lines (RILs) with a Rag2-Rsv1-h gene haplotype in coupling phase using resistance alleles from two different genetic sources (PI 243540 (Rag2) and Suweon 97 (Rsv1-h)), (ii) confirm phenotypically the resistant reaction against both pests in double-resistant RILs, and (iii) dissect the Rag2-Rsv1-h region with molecular markers and investigate the potential for structural variation.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Results: &lt;/strong&gt;We observed a recombination event in identified double-resistant F&lt;sub&gt;3:5&lt;/sub&gt; RILs in a region of chromosome 13 ca. 21 kb long (between positions 30,297,227 and 30,318,949 in Wm82.a2.v1) that lies between the reported locations of the Rsv1-h and Rag2 genes (29,815,463--29,912,369 and 30,412,581--30,466,533 intervals, respectively, based on Wm82.a2.v1), indicating the double-resistant haplotype is in coupling phase. The tight LD estimates obtained between haplotype markers underscored the physical proximity of the two resistance genes. Only 10 recombinant haplotype classes (excluding double heterozygotes) were observed among the 51 that were possible with a four loci haplotype. The 10 recombinant classes represented 15 out of 192 screened individuals. A joint SMV-aphid phenotypic greenhouse screen allowed us to identify the best aphid biotype 1 and SMV-G1, double resistant haplotype class in recombinant progeny. Our molecular marker results agree with previous fine-mapping reports and preclude the presence of resistance genes other than Rag2 and Rsv1-h in double-resistant RILs. A comparative genomic hybridization analysis revealed no obvious structural variants in the region.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Conclusions: &lt;/strong&gt;To our knowledge, this is the first report of double-resistant Rag2-Rsv1-h soybean RILs that used a plant-insect-pathogen tritrophic system for germplasm enhancement. The co-occurrence of Rag and Rsv genes in a region that clusters resistance genes on chromosome 13 may be a unique feature of domesticated soybean. The recombinant genotypes will be useful in breeding to develop soybean cultivars with resistance to both the vector and the virus. The parental and recombinant genotypes may be helpful in future studies to elucidate interesting evolutionary questions regarding vector, ","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"539"},"PeriodicalIF":3.5,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12117769/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144156872","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":"Implementation of NGS and SNP microarrays in routine forensic practice: opportunities and barriers.","authors":"Sharlize Pedroza Matute, Sasitaran Iyavoo","doi":"10.1186/s12864-025-11723-6","DOIUrl":"10.1186/s12864-025-11723-6","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"541"},"PeriodicalIF":3.5,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12117683/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144172148","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}