GenomePub Date : 2025-01-01DOI: 10.1139/gen-2024-0153
Alex M V Ferreira, Patrik F Viana, Leandro Marajó, Eliana Feldberg
{"title":"Chromosomal and molecular perspectives on <i>Potamotrygon motoro</i> (Müller & Henle, 1841) from central Amazon.","authors":"Alex M V Ferreira, Patrik F Viana, Leandro Marajó, Eliana Feldberg","doi":"10.1139/gen-2024-0153","DOIUrl":"10.1139/gen-2024-0153","url":null,"abstract":"<p><p>Cytogenetic studies on <i>Potamotrygon motoro</i> (Müller & Henle, 1841) are limited to classical cytogenetic techniques, but they do reveal great karyotypic variation. The main differences are related to the karyotypic formula and the absence/presence of sex chromosome systems. Thus, this study aimed to expand knowledge of the karyotypic composition of <i>Potamotrygon motoro</i> from different locations of the Central Amazon using Fluorescence in situ Hybridization to investigate the distribution of ribosomal DNAs (rDNA) and microsatellites sequences (SSRs). In addition, we used the mitochondrial DNA cytochrome oxidase subunit I (mtDNA COI) to perform neighbor-joining analysis to investigate the relationships among the individuals sampled. In our study, <i>Potamotrygon motoro</i> presented 2n = 66 chromosomes, with 18m + 12sm + 10st + 26a and heterochromatic blocks on centromeric region of all chromosomes. The 18S rDNA is present in three chromosomal pairs and 5S rDNA is located in the pair 16, which is a feature shared among freshwater stingray species. Regarding the mapping of SSRs, dinucleotide sequences showed a greater number of sites, usually on terminal regions of chromosomal pairs, with an accumulation throughout the long arms of the pair 17. Our molecular analyses did not reveal differences between the sequences used. In general, the karyotypic differences previously reported for <i>Potamotrygon motoro</i> indicate the presence of different cytotypes within the species.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":"68 ","pages":"1-9"},"PeriodicalIF":2.3,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143499364","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
GenomePub Date : 2025-01-01DOI: 10.1139/gen-2025-0017
Mizanur Rahaman, Stephen E Strelkov, Hao Hu, Fuyou Fu, Fengqun Yu
{"title":"A second gene for resistance to four pathotypes of <i>Plasmodiophora brassicae</i> identified in the <i>Brassica napus</i> cultivar 'Mendel'.","authors":"Mizanur Rahaman, Stephen E Strelkov, Hao Hu, Fuyou Fu, Fengqun Yu","doi":"10.1139/gen-2025-0017","DOIUrl":"10.1139/gen-2025-0017","url":null,"abstract":"<p><p>Clubroot, caused by the obligate parasite <i>Plasmodiophora brassicae</i>, poses a significant threat to the Canadian canola industry, resulting in substantial yield losses. Genetic resistance is an effective strategy for managing the disease. In this study, 137 doubled haploid (DH) lines derived from the European oilseed rape cultivar 'Mendel' were phenotyped against <i>P. brassicae</i> pathotypes 3D, 5C, and 8J, which are aggressive toward the first-generation clubroot-resistant canola cultivars, and were genotyped using genotyping-by-sequencing. Disease severity indices in the population were highly correlated among the three pathotypes, with correlation coefficients of <i>r</i> ≥ 0.82. In the DH population, 2642 high-quality Single nucleotide polymorphisms were detected by employing the <i>Brassica napus</i> 'ZS11' reference genome. A single quantitative trait locus, <i>Rcr3</i><sup>Mendel</sup>, was detected and mapped to a 317 kb region on chromosome A08, flanked by the markers ZS_A08_15999175 and ZS_A08_16316110. Within this region, 43 genes were identified, including a single Toll interleukin-1 receptor nucleotide-binding site-leucine-rich repeat (TNL) gene, <i>BnaA08T0102200ZS</i>. This region is homologous to the 13 415 472-15 791 728 bp region of chromosome A08 in <i>Brassica rapa</i> ECD 04, the donor of clubroot resistance in 'Mendel'. Two TNL genes, <i>BraA08g039211E</i> and <i>BraA08g039212E</i>, were identified in the ECD 04 genome. Kompetitive allele-specific PCR analysis identified eight markers that co-segregated with <i>Rcr3</i><sup>Mendel</sup>. Resistance to pathotype 3H was also found to co-segregate with resistance to pathotypes 5C, 3D, and 8J.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-12"},"PeriodicalIF":1.7,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144325301","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
GenomePub Date : 2025-01-01DOI: 10.1139/gen-2025-0007
Cynthia Gagné-Thivierge, Marie-Lou Gauthier, Martine Denicourt, Marie-Ève Lambert, Antony T Vincent, Steve J Charette
{"title":"Diversity of <i>tet</i>(L)-bearing plasmids found in Eastern Canadian <i>Staphylococcus hyicus</i> isolates from swine.","authors":"Cynthia Gagné-Thivierge, Marie-Lou Gauthier, Martine Denicourt, Marie-Ève Lambert, Antony T Vincent, Steve J Charette","doi":"10.1139/gen-2025-0007","DOIUrl":"10.1139/gen-2025-0007","url":null,"abstract":"<p><p><i>Staphylococcus hyicus</i> is the etiological agent of exudative epidermitis (EE) in suckling and weaned piglets, which is an endemic disease of concern for animal health and welfare on swine farms. <i>Staphylococcus hyicus</i> is not widely studied, and there is no recent scientific literature on Canadian strains. In a preliminary study, we presented an Eastern Canadian <i>S. hyicus</i> strain isolated from an EE case and bearing a plasmidic <i>tet</i>(L) gene conferring resistance to tetracyclines, one of the most commonly used antibiotics in Canadian swine farms. The current study characterized the <i>tet</i>(L)-bearing plasmids present in <i>S. hyicus</i> isolates from pigs in Eastern Canadian to better understand the potential vectors for this gene dissemination. Eleven <i>S. hyicus</i> isolates harboring <i>tet</i>(L) as the only tetracycline resistance gene were sequenced using Oxford Nanopore Technology and analyzed. Eight different <i>tet</i>(L)-bearing plasmids were identified that share similarities with <i>Staphylococcus aureus</i> sequences available in the National Center for Biotechnology Information. Only one of the plasmids was present in more than one isolate and two isolates carried <i>tet</i>(L) on their chromosome. This suggests a high diversity of <i>tet</i>(L)-bearing plasmids in <i>S. hyicus</i> and the possible need to analyze swine farm samples over time to understand the dynamics of <i>tet</i>(L) in <i>S. hyicus</i>.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-7"},"PeriodicalIF":1.7,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145006046","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
GenomePub Date : 2025-01-01DOI: 10.1139/gen-2024-0162
Kartik Juyal, Heena Devkar, Aabha Deshpande, Narsinh L Thakur
{"title":"Genome assembly, analysis, and mining of <i>Kocuria flava</i> NIO_001: a thiopeptide antibiotic synthesizing bacterium isolated from marine sponge.","authors":"Kartik Juyal, Heena Devkar, Aabha Deshpande, Narsinh L Thakur","doi":"10.1139/gen-2024-0162","DOIUrl":"10.1139/gen-2024-0162","url":null,"abstract":"<p><p>Genome mining has been a key strategy for finding biosynthetic gene clusters (BGCs) coding for secondary metabolites in the recent past. Actinomycetia is among the important bacterial classes found in marine habitats, renowned for producing high-value secondary metabolites. <i>Kocuria</i> is one such gram-positive bacteria that has been reported to produce the potent antibacterial molecule kocurin/PM181104. The objective of this study was to confirm the production of kocurin/PM181104 followed by sequencing, assembly, and mining of the genome of <i>Kocuria flava</i> NIO_001. AntiSMASH analysis predicted the BGCs involved in the production of kocurin along with eight promising secondary metabolite-producing BGCs including non-alpha poly-amino acids like e-polylysin (NAPAA), ribosomally synthesized and post-translationally modified peptide like (RiPP-like), non-ribosomal peptide synthetase like (NRPS-like), NRPS-independent IucA/IucC-like siderophores (NI-siderophore), type III polyketide synthase (T3PKS), ε-Poly-l-lysine (NAPAA), terpene, and betalactone. Kyoto Encyclopedia for Genes and Genomes pathway analysis showed the presence of biosynthetic pathways involved in terpenoid backbone synthesis and the presence of certain hemolysin-like proteins. The present investigation is highly valuable for designing experiments to overproduce this potent antibiotic molecule by using a reverse engineering approach.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-10"},"PeriodicalIF":2.3,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143624311","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
GenomePub Date : 2025-01-01DOI: 10.1139/gen-2024-0096
Caio T Rodrigues Correa, Magdalena Vaio, Sanzio C L Barrios, Cacilda B do Valle, Giovana A Torres, Vânia H Techio
{"title":"The repetitive DNA landscape in the <i>brizantha</i> agamic complex of <i>Urochloa</i> P. Beauv.","authors":"Caio T Rodrigues Correa, Magdalena Vaio, Sanzio C L Barrios, Cacilda B do Valle, Giovana A Torres, Vânia H Techio","doi":"10.1139/gen-2024-0096","DOIUrl":"10.1139/gen-2024-0096","url":null,"abstract":"<p><p><i>Urochloa</i> P. Beauv. (formerly classified as <i>Brachiaria</i> (Trin.) Griseb<i>.</i>) is a genus of African perennial grasses that is extensively cultivated in tropical countries for cattle nutrition. Three of the most economically relevant species, <i>Urochloa brizantha, Urochloa decumbens</i>, and <i>Urochloa ruziziensis</i>, form the <i>brizantha</i> agamic complex, which includes allopolyploid series with distinct subgenomes. Investigating the composition and organization of repetitive DNA, a major component of grass genomes, can provide insights into their genomic relationships and evolutionary history. This study aimed to characterize the repetitive DNA landscape of selected <i>Urochloa</i> species belonging to the <i>b</i> <i>rizantha</i> agamic complex; identify and compare major repeat classes across species; and evaluate their potential as cytogenetic markers on mitotic chromosomes using fluorescent <i>in situ</i> hybridization (FISH). Clustering analysis revealed that repetitive DNA constitutes 56%-65% of the genomes, with Ty3/Gypsy retrotransposons, particularly the <i>Athila</i> and <i>Retand</i> lineages, representing the most abundant repeat class. <i>Urochloa decumbens</i> exhibited the highest proportion of Ty3/Gypsy retrotransposons, while <i>U. ruziziensis</i> had the highest satellite DNA content. The chromosomal location of representative satellites (UroSat-1a, UroSat-2a, and UroSat-3) was determined in all three species via FISH. UroSat-1a was detected in all centromeres, while UroSat-2a and UroSat-3 signals varied in number and position. Our findings validate the use of satDNA as cytogenetic markers in the <i>brizantha</i> agamic complex of <i>Urochloa</i> and revealed genomic relationships among different species and ploidy levels.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-13"},"PeriodicalIF":2.3,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143070848","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
GenomePub Date : 2025-01-01DOI: 10.1139/gen-2025-0003
Arash Mohammadi Matak, Yizhu Mu, Seyedeh Mahdiye Mohati, Stephanie Makdissi, Francesca Di Cara
{"title":"Circadian rhythm and immunity: decoding chrono-immunology using the model organism <i>Drosophila melanogaster</i>.","authors":"Arash Mohammadi Matak, Yizhu Mu, Seyedeh Mahdiye Mohati, Stephanie Makdissi, Francesca Di Cara","doi":"10.1139/gen-2025-0003","DOIUrl":"10.1139/gen-2025-0003","url":null,"abstract":"<p><p>Circadian rhythms are important cellular pathways first described for their essential role in helping organisms adjust to the 24 h day-night cycle and synchronize physiological and behavioral functions. Most organisms have evolved a circadian central clock to anticipate daily environmental changes in light, temperature, and mate availability. It is now understood that multiple clocks exist in organisms to regulate the functions of specific organs. Epidemiological studies in humans reported that disruption of the circadian rhythms caused by sleep deprivation is linked to the onset of immune-related conditions, suggesting the importance of circadian regulation of immunity. Mechanistic studies to define how circadian clocks and immune responses interact have profound implications for human health. However, elucidating the clocks and their tissue-specific functions has been challenging in mammals. Many studies using simple model organisms such as <i>Drosophila melanogaster</i> have been pioneering in discovering that the clock controls innate immune responses and immune challenges can impact circadian rhythms and/or their outcomes. In this review, we will report genetic studies using the humble fruit fly that identified the existence of reciprocal interactions between the circadian pathway and innate immune signaling, contributing to elucidate mechanisms in the growing field of chrono-immunology.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-18"},"PeriodicalIF":2.3,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143763889","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
GenomePub Date : 2025-01-01Epub Date: 2024-09-03DOI: 10.1139/gen-2023-0130
Linda Inês Silveira, Gisele Amaro Teixeira, Luísa Antônia Campos Barros, Jorge Abdala Dergam, Hilton Jeferson Alves Cardoso de Aguiar
{"title":"Chromosomal diversity in <i>Crematogaster</i> Lund, 1831 (Formicidae: Myrmicinae) from the Amazon rainforest.","authors":"Linda Inês Silveira, Gisele Amaro Teixeira, Luísa Antônia Campos Barros, Jorge Abdala Dergam, Hilton Jeferson Alves Cardoso de Aguiar","doi":"10.1139/gen-2023-0130","DOIUrl":"10.1139/gen-2023-0130","url":null,"abstract":"<p><p><i>Crematogaster</i> Lund, 1831 is a speciose ant genus globally distributed and easily recognizable. Although biogeographical theories explain some variation among Neotropical <i>Crematogaster</i>, several taxonomical issues remain unresolved. While cytogenetic approaches can help to delimit species, cytogenetic data are only available for 18 taxa. In this study, classical and molecular cytogenetic analyses were performed on five <i>Crematogaste</i>r species from the Brazilian Amazon to identify species-specific patterns. Two different cytotypes, both with 2<i>n</i> = 22 chromosomes were observed in <i>Crematogaster erecta</i> Mayr, 1866, suggesting the presence of cryptic species, although with different karyotypic formulas. <i>Crematogaster</i> aff. <i>erecta</i> had 2<i>n</i> = 28, while <i>Crematogaster limata</i> Smith, 1858, <i>Crematogaster tenuicula</i> Forel, 1904, and <i>Crematogaster</i> sp. had 2<i>n</i> = 38. The telomeric motif (TTAGG) <i><sub>n</sub></i> was found in all five species, and the (TCAGG) <i><sub>n</sub></i> motif was detected in the telomeres of <i>C. limata</i>. This peculiar motif was also detected in the centromeric regions of <i>C. erecta</i> cytotype I. The microsatellite (GA) <i><sub>n</sub></i> was dispersed in the chromosomes of all species studied, which also had a single intrachromosomal rDNA site. The cytogenetic results revealed notable interspecific and intraspecific variation, which suggests different chromosomal rearrangements involved in the origin of these variations, also highlighting the taxonomic value of cytogenetic data on <i>Crematogaster</i>.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-12"},"PeriodicalIF":2.3,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142125506","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
GenomePub Date : 2025-01-01DOI: 10.1139/gen-2024-0180
Christine L Ouellet-Fagg, Anne A Easton, Kevin J Parsons, Cameron M Nugent, Roy G Danzmann, Moira M Ferguson
{"title":"The evolution of genomic organization through chromosomal rearrangements in Arctic charr (<i>Salvelinus alpinus</i>).","authors":"Christine L Ouellet-Fagg, Anne A Easton, Kevin J Parsons, Cameron M Nugent, Roy G Danzmann, Moira M Ferguson","doi":"10.1139/gen-2024-0180","DOIUrl":"https://doi.org/10.1139/gen-2024-0180","url":null,"abstract":"<p><p>Chromosomal rearrangements (CRs) can play an important role in evolutionary diversification by preserving linkage among favourable alleles through reduced recombination and/or by reducing hybrid fitness due to genomic incompatibilities. Our goal was to determine to what extent CRs contribute to known patterns of genetic variation in Arctic charr (<i>Salvelinus alpinus</i>). To address this goal, we compared genetic linkage maps to identify whole arm CRs and smaller scale structural variants (SVs) such as translocations/transpositions and inversions found in groups of populations that reflect the temporal sequence of geographic isolation events. If CRs contribute to genetic differentiation, we expected that CRs would be specific to glacial lineages, geographic clusters of populations within lineages, and sympatric morphs. We detected fusions and fissions of whole chromosome arms and SV involving translocations/transpositions of the sex-determining gene (<i>sdY</i>) and inversions. Several CRs were shared across populations from the Arctic and Atlantic glacial lineages, Canadian and Icelandic populations within the Atlantic lineage, between two Icelandic populations and sympatric morphs within Icelandic populations, suggesting that their origin predates geographic isolation in glacial refugia. Other CRs were specific to single populations, which suggests a more recent origin of these variants in refugia, during post-glacial recolonization and/or in contemporary populations. Thus, CRs contribute relatively little to known patterns of genetic differentiation at different geographic scales but represent a pool of standing genetic variation for evolution.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":"68 ","pages":"1-19"},"PeriodicalIF":2.3,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144011729","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
GenomePub Date : 2025-01-01DOI: 10.1139/gen-2025-0010
S E Weber, L Roscher-Ehrig, S Zanini, G Yildiz, A Abbadi, T Kox, A A Golicz, R J Snowdon
{"title":"Single-cross prediction with imputed multiomic data: a case study in rapeseed.","authors":"S E Weber, L Roscher-Ehrig, S Zanini, G Yildiz, A Abbadi, T Kox, A A Golicz, R J Snowdon","doi":"10.1139/gen-2025-0010","DOIUrl":"10.1139/gen-2025-0010","url":null,"abstract":"<p><p>Advancements in sequencing technologies enabled the assembly and characterization of plant genomes with high resolution. In breeding programs, these data are combined with phenotypic information in genomic prediction to select genotypes based on their genetic profiles. Although single nucleotide polymorphism (SNP) arrays are commonly used for genotyping, they capture only a fraction of the genomewide diversity. To address this, one approach involves genotyping the entire population with arrays, sequence a subset using whole-genome sequencing (WGS), or assessing gene expression profiles, followed by imputing the data across the entire population. This study evaluates the effect of imputed WGS markers (SNPs and structural variants) and expression data on genomic prediction in a rapeseed hybrid breeding population. A combination of SNP arrays, WGS, and RNA sequencing was employed, followed by imputation of marker and expression data. Genomic prediction was utilized to estimate general and specific combining ability effects in untested hybrids. However, while adding imputed whole-genome and expression data increased marker density and linkage disequilibrium, it did not enhance prediction accuracy compared to SNP array data. This is attributed to redundancy in relationship, imputation errors, or environmental influences on gene expressions. This suggests that SNP arrays continue to be reliable for genomic prediction in rapeseed hybrid breeding.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-17"},"PeriodicalIF":2.3,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144009011","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
GenomePub Date : 2025-01-01DOI: 10.1139/gen-2024-0182
Kawalpreet Kaur, Urmila Basu, Nat N V Kav, Habibur Rahman
{"title":"Transcriptome analysis of <i>Brassica napus</i> near-isogenic lines carrying clubroot resistance from turnip (<i>Brassica rapa</i> var. <i>rapifera</i>).","authors":"Kawalpreet Kaur, Urmila Basu, Nat N V Kav, Habibur Rahman","doi":"10.1139/gen-2024-0182","DOIUrl":"10.1139/gen-2024-0182","url":null,"abstract":"<p><p>Understanding the intricate molecular interplay between Brassica hosts and the pathogen <i>Plasmodiophora brassicae</i>, causative agent of clubroot disease, is pivotal for devising effective resistance to this disease in Brassica crops. While existing transcriptomic studies have elucidated the host responses to pathogen infection, a comprehensive analysis employing near-isogenic lines (NILs) remains imperative for better understanding of the resistance mechanisms. In this study, we conducted a comparative transcriptome profiling utilizing clubroot-susceptible (CS) and clubroot-resistant (CR) NILs of <i>Brassica napus</i>, carrying the clubroot resistance of turnip (<i>Brassica rapa</i> var. <i>rapifera</i>), at 7 and 14 days after inoculation. We observed the upregulation of the genes governing phytohormone signaling, receptor kinases, transcription factors, calcium fluxes, and glucosinolate metabolism in the CR-NILs. Notably, we identified defense-related genes associated with jasmonic acid signaling (<i>JAZ2</i>), calcium signaling (<i>CNGC</i>s, <i>GLR</i>s), receptor kinases (<i>WAK</i>s), and glucosinolate biosynthesis (<i>APK</i>; <i>GST</i>s, also involved in ROS homeostasis) that may play pivotal roles in resistance. One of the important novel findings was the association of the <i>JAZ2</i> gene with clubroot resistance in <i>B. napus</i>. This study also highlighted the upregulation of NLRs (RNLs and TNLs) and ERF transcription factors, offering new insights into the molecular mechanisms of clubroot resistance in <i>B. napus</i>. Additionally, we observed the upregulation of pathogenesis-related proteins (PR-3 and PR-4) and WRKY transcription factors (<i>WRKY62, WRKY70</i>), suggesting a coordinated response involving multiple layers of immunity. Based on our results, we propose a comprehensive model delineating the molecular events potentially contributing to clubroot resistance in <i>B. napus</i> CR-NILs. Our findings have contributed to an enhanced understanding of the potential mechanisms involved in clubroot resistance, which may have utility in targeted breeding initiatives to mitigate the threat of clubroot disease in Brassica crops including canola.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-17"},"PeriodicalIF":1.7,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144247486","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}