Theoretical and Applied Genetics最新文献

{"title":"Non-linear kernel methods for genomic prediction of soybean yield and quality in multi-environment trials.","authors":"Wanessa Alves Lima Paiva, Weverton Gomes da Costa, Leandro Pacheco Machado, Ana Carolina Campana Nascimento, Diego Jarquin, Moyses Nascimento","doi":"10.1007/s00122-026-05387-3","DOIUrl":"10.1007/s00122-026-05387-3","url":null,"abstract":"<p><strong>Key message: </strong>Nonlinear kernels improve the accuracy of genomic prediction while preserving the inferential framework of quantitative genetics. Improving the predictive accuracy of genomic prediction (GP) for complex genetic architectures involving non-additive effects and genotype-by-environment interactions (GEI) requires alternative approaches beyond conventional linear models such as Genomic Best Linear Unbiased Prediction (GBLUP). In this study, we evaluated grain yield, protein content, and oil content in the SoyNAM population, comprising 1,379 genotypes evaluated across six environments, to compare four non-linear kernels (Laplacian, Gaussian, Bessel, and Polynomial) with the GBLUP and Random Forest a Machine Learning model. Two variance structures (main effects and main plus interaction effects) were evaluated under three cross-validation schemes: CV1 (predicting untested genotypes in observed environments), CV2 (predicting tested genotypes in observed environments), and CV0 (predicting tested genotypes in unobserved environments). In addition, we tested the same models in a epistatic trait simulated dataset. The inclusion of GEI effects substantially improved predictive accuracy for grain yield under CV1 and CV2, whereas only modest gains were observed for protein and oil content. Across traits and validation schemes, the nonlinear kernels consistently matched or outperformed GBLUP, with the greatest advantage observed for oil content and under the CV0 scheme. No single nonlinear kernel consistently outperformed the others, indicating that kernel performance was environment dependent. Compared with Random Forest, the non-linear kernels achieved comparable or superior predictive accuracy while preserving the mixed-model framework, enabling the estimation of variance components. Moreover, in the extra dataset, the Laplacian kernel consistently showed high predictive accuracy across all scenarios, supporting its use as a promising option to the widely used Gaussian kernel. Therefore, non-linear kernel methods provide a robust and interpretable alternative for GP.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"139 10","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13601130/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149031365","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic identification and characterization of a locus controlling productive tiller number with breeding value in Chinese endemic wheat.","authors":"Tongzhu Wang, Jiating Chen, Xinrong Hu, Md Nahibuzzaman Lohani, Huaping Tang, Yanlin Liu, Qiang Xu, Yunfeng Jiang, Qiantao Jiang, Guoyue Chen, Yuming Wei, Jian Ma","doi":"10.1007/s00122-026-05391-7","DOIUrl":"10.1007/s00122-026-05391-7","url":null,"abstract":"<p><strong>Key message: </strong>This study identified and validated novel PTN QTL and predicted corresponding candidate genes, providing a genetic basis for the improvement of tiller number and grain yield in wheat. Productive tiller number (PTN) is a central component of wheat yield, yet its genetic regulation remains complex and highly responsive to environmental variation. This study employed a Chinese endemic wheat association population of 182 accessions to systematically dissect the genetic architecture of PTN across three environments. Phenotypic analysis revealed moderate-to-high genetic control (H² = 69.59%) coupled with evident genotype-environment interactions. Genome-wide association mapping identified a major locus, QPTN.sicau-CEW-5D, which accounted for 70.6% of the significant associations and harbored four distinct haplotypes. The favorable Hap1 exhibited significantly higher PTN and plant height but with no significant differences on spike length and spikelet number per spike across multiple environments, suggesting its great potential in enhancing grain yield Validation in an independent population comprising 220 Sichuan wheat cultivars and landraces confirmed the highly significant and stable effect of QPTN.sicau-CEW-5D, in sharp contrast to the environment-dependent performance of loci on chromosomes 3A and 6A. Through candidate gene analysis integrating non-synonymous variant screening and independent association testing, we prioritized two receptor-like protein kinase (RLK) genes (TraesCS5D02G556900 and TraesCS5D02G557800) and one NLR gene (TraesCS5D02G557600) as key regulators of PTN variation. These findings provide novel insights into the genetic basis governing wheat tiller development and offer reliable genomic targets and superior haplotypes for marker-assisted breeding.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"139 10","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149031419","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An integrated molecular cytogenetic platform enables precise characterization of Thinopyrum ponticum chromatin and its structural modifications in wheat background.","authors":"Chengzhi Jiang, Min Wan, Jun Wang, Yimin Ren, Ennian Yang, Guangrong Li, Peng Zhang, Zujun Yang","doi":"10.1007/s00122-026-05392-6","DOIUrl":"10.1007/s00122-026-05392-6","url":null,"abstract":"<p><strong>Key message: </strong>By integrating ND‑FISH, Oligo‑FISH painting, and chromosome microdissection, we established a comprehensive platform for decaploid Thinopyrum ponticum, enabling karyotyping, sequencing, and marker development, which provides precise tools for the targeted introgression and utilization of alien chromatin in wheat breeding. Thinopyrum ponticum (Podp.) Barkworth & D.R. Dewey, a decaploid wild relative of wheat, represents a valuable genetic reservoir for improving abiotic stress tolerance and disease resistance in wheat breeding. However, its complex genome structure and polyploid nature have long impeded both precise genome assembly and comprehensive characterization of individual chromosomes for wheat-Thinopyrum introgressions. In the present study, we established a reference karyotype of individual Th. ponticum chromosomes by integrated cytogenetic methods combining non‑denaturing fluorescence in situ hybridization (ND‑FISH) and bulked oligonucleotide pool‑based FISH (Oligo‑FISH) painting. This platform was subsequently applied to cytogenetically analyze the wheat-Th. ponticum partial amphiploid 'Agrotana'. Immunostaining assays revealed that Thinopyrum chromosomes maintain normal centromeric histone localization and exhibit distinct methylation patterns in the wheat background. The group-6 chromosomes of the Thinopyrum species harbor several superior resistance genes, we performed microdissection and sequencing of Th. ponticum 6J^SS chromosome, generating a genomic resource that enables both comparative genome analysis and targeted functional gene discovery. The specificity of Thinopyrum introgressions in various wheat-Thinopyrum derivatives was further validated by seed storage protein profiles. Collectively, this study establishes an integrated molecular and cytogenetic platform for the accurate identification and assembly of Thinopyrum chromatin, thereby accelerating the targeted introgression and effective deployment of its agronomically valuable traits in wheat improvement programs.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"139 10","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149031367","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"SlTCP16 confers disease resistance in tomato via a dual regulatory mechanism involving transcriptional activation and protein interaction with Sl4CL3.","authors":"Chunxin Liu, Yurong Yang, Yue Wang, Zhentong Zhao, Weiman Sun, He Zhang, Dalong Li, Tingting Zhao, Xiangyang Xu","doi":"10.1007/s00122-026-05390-8","DOIUrl":"10.1007/s00122-026-05390-8","url":null,"abstract":"<p><strong>Key message: </strong>Our study revealed that SlTCP16 can transcriptional activation and interaction with Sl4CL3, thereby enhancing the tomato's resistance toPstDC3000. This resistance is associated with an increased accumulation of lignin. Lignin deposition serves as a critical physical barrier against bacterial pathogens. However, the precise regulatory networks orchestrating this defense response in tomato remain incompletely understood. We identify the transcription factor SlTCP16 as a novel positive regulator of tomato immunity against Pseudomonas syringae pv. tomato (Pst DC3000). We show that Pst DC3000 infection strongly induces SlTCP16 expression. Functionally, SlTCP16 overexpression significantly reduced reactive oxygen species (ROS) accumulation and bolstered disease resistance, while SlTCP16 knockout mutants showed the opposite performance. Mechanistically, we uncover a dual regulatory mode, SlTCP16 not only directly activates the transcription of the lignin biosynthetic gene Sl4CL3 by binding to its promoter but also physically interacts with the Sl4CL3 protein. Sl4CL3 acts downstream of SlTCP16, and overexpression of Sl4CL3 enhanced disease resistance in the sltcp16 mutant. Collectively, our data suggest that SlTCP16 contributes to disease resistance by regulating Sl4CL3 through transcriptional activation and protein-protein interaction. This regulatory module is associated with increased lignin accumulation.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"139 10","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149031356","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of stable QTL for yield-related traits in a durum wheat Svevo × Zavitan RIL population.","authors":"Xinli Zhou, Bingchuan Zhou, Guihua Zhang, Gaoying Zou, Xudong Yang, Chongjing Xia, Xin Li, Shouhang Zheng, Yong Ren","doi":"10.1007/s00122-026-05389-1","DOIUrl":"10.1007/s00122-026-05389-1","url":null,"abstract":"<p><strong>Key message: </strong>Yield-component QTL mapping in a Svevo × Zavitan durum wheat RIL population identifies 11 stable loci across four environments and prioritizes 67 and 88 high-confidence candidate genes linked to grain development and regulatory pathways, providing markers and targets for yield improvement. Wheat is a cornerstone of global food security. Durum wheat (Triticum turgidum ssp. durum), domesticated from wild emmer wheat (Triticum turgidum ssp. dicoccoides), represents a valuable genetic reservoir for improvement. To decipher the genetic architecture of yield components, a population of 135 recombinant inbred lines (RILs) derived from a cross between the elite durum wheat cultivar Svevo (female) and wild emmer wheat accession Zavitan (male) was evaluated for grain length (GL), grain width (GW), grain length-width ratio (LWR), and thousand-grain weight (TGW) across four environments. Genotyping was performed using the wheat 90 K single nucleotide polymorphism (SNP) array and subsequent quantitative trait locus (QTL) analysis revealed 11 stable QTL, with physical intervals ranging from 0.7 to 15.6 Mb in the durum wheat reference genome. Among these, three QTL for GL (QGLsv.swust-5AL, QGLsv.swust-5BL, and QGLsv.swust-7AL), two for GW (QGWsv.swust-4AL and QGWsv.swust-5AL), and two for TGW (QTGWsv.swust-2BL and QTGWsv.swust-5BL) carried positive alleles from the cultivated parent Svevo. Conversely, all four QTL for LWR (QLWRzv.swust-2BS, QLWRzv.swust-4AL, QLWRzv.swust-4BL, and QLWRzv.swust-6AS) were contributed by the wild parent Zavitan. Collectively, these QTL explained 9.22% to 19.22% of the phenotypic variation. Projection of the QTL intervals onto the Chinese Spring, Svevo, and Zavitan reference genomes identified 67, 88, and 70 high-confidence candidate genes, respectively. Functional annotation associated these genes with seed development, transcription regulation, hormone signaling, ubiquitin-mediated proteolysis, and carbohydrate metabolism. This study highlight the complementary genetic contributions from both cultivated and wild gene pools. The identified QTL and candidate genes provide a direct resource for marker-assisted breeding, demonstrating the utility of interspecific crosses to enrich the genetic basis for yield enhancement in durum wheat.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"139 10","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149031375","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Aphanomyces euteiches causes disease in Lathyrus sativus with a globally diverse, polygenic resistance landscape.","authors":"Sara Rodriguez-Mena, Mario González, Ehsan Valiollahi, Carmen Santos, Diego Rubiales, Maria Carlota Vaz Patto","doi":"10.1007/s00122-026-05372-w","DOIUrl":"10.1007/s00122-026-05372-w","url":null,"abstract":"<p><strong>Key message: </strong>Aphanomyces euteiches inoculation of a global Lathyrus sativus collection allowed the identification of sources of resistance and associated candidate genes. Aphanomyces euteiches is a major concern in legume crops with limited efficient methods for its management. Although Aphanomyces root rot has been widely studied in pea and lentil, the effect of this pathogen on grass pea (Lathyrus sativus) has been poorly explored. This study aimed to characterise the response of a globally diverse grass pea collection to A. euteiches and to identify genomic regions associated with any potential resistance. A diverse panel of 169 grass pea accessions was inoculated with the A. euteiches RB84 isolate. Twenty days after inoculation, foliar and root symptoms were evaluated. A wide range of responses was observed within the panel, from susceptibility to partial or even complete resistance. Along with these phenotypic data, an improved acquired 12,974 single-nucleotide polymorphism (SNP) data set was used to perform a genome-wide association study. The association study identified 20 resistance-associated SNPs, across five of the seven grass pea chromosomes, suggesting a polygenic nature. In silico analysis identified seven putative candidate genes associated with resistance involved in vesicle trafficking, signal transduction, nucleotide metabolism, fatty-acid metabolism, cell wall synthesis and ethylene signalling. This study confirms the compatible grass pea × A. euteiches interaction, identifying for the first time, sources of resistance and proposing resistance-associated loci with co-located candidate genes for future precision breeding purposes.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"139 10","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13593742/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149017999","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Twenty-one years of three-way hybrid breeding shaped diversity and complementarity of male and female gene pools in sugar beet.","authors":"Augustin Desprez, Karine Henry, Bruno Desprez, Pierre Devaux, Alain Charcosset, Maud I Tenaillon, Laurence Moreau","doi":"10.1007/s00122-026-05366-8","DOIUrl":"10.1007/s00122-026-05366-8","url":null,"abstract":"<p><strong>Key message: </strong>Three-way hybrid breeding in sugar beet is associated with strong genomic differentiation between male and female parental pools and persistent haplotypic differentiation at agronomically relevant loci over the last two decades. Three-way hybrid breeding has been used in several major crops to increase seed yield and manage heterosis. Sugar beet (Beta vulgaris ssp. vulgaris) breeding relies exclusively on it and combines cytoplasmic male sterility (CMS) and monogermity to exploit heterosis by combining male and female parental pools. The genomic consequences of this breeding scheme remain poorly characterized. We assembled a unique dataset comprising 1285 accessions spanning 21 years of selection within a breeding program, genotyped for 10,033 SNPs, to investigate genetic structuring and selection dynamics. Principal component and admixture analyses revealed a clear differentiation between parental pools. Over 21 years, males displayed a significant decline in within-pool diversity, accompanied by a rise in inter-pool differentiation. Linkage disequilibrium decreased in recent male lines, reflecting breeding practices that increase allele shuffling. Selection scans identified 174 outlier SNPs differentiating pools. Outliers clustered into seven haploblocks, including a region encompassing rhizomania-resistance gene (Rz1) and, more surprisingly, a region encompassing the domestication bolting locus B (BvBTC1). These results demonstrate that over the last 21 years, three-way hybrid breeding has increased differentiation between heterotic pools and shaped haplotypic variation at agronomically relevant loci, providing a genomic basis for future evaluation of their effects on agronomic performance.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"139 10","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13589703/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149008864","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Improving multi-trait genomic prediction using synthetic traits from hyperspectral data based on co-heritability.","authors":"Ashmita Upadhyay, Ruhana Azam, Meilu Yuan, Stefan Ivanovic, John N Ferguson, Rachel E Paul, Sanmi Koyejo, Mohammed El-Kebir, Alexander E Lipka, Andrew D B Leakey, Samuel B Fernandes","doi":"10.1007/s00122-026-05334-2","DOIUrl":"10.1007/s00122-026-05334-2","url":null,"abstract":"<p><strong>Key message: </strong>Synthetic traits, wavelength ratios selected by co-heritability, raised multi-trait genomic predictive ability for leaf nitrogen and specific leaf area in sorghum by up to 17% over single-trait models. Genomic prediction (GP) is an essential tool in plant breeding as it can accelerate cultivar development by predicting the performance of unphenotyped lines. When using single-trait GP models, the precision of prediction is constrained by the heritability of the target trait. Multi-trait genomic prediction can be used to improve accuracy but requires identifying secondary traits with high heritability and genetic correlation with target traits. This study assessed the efficiency of multi-trait genomic prediction models powered by secondary traits derived from high-throughput phenotyping data when predicting leaf nitrogen content (N) and specific leaf area (SLA) in diverse sorghum accessions. We hypothesized that wavelength ratios from hyperspectral data could serve as synthetic secondary traits. Therefore, we developed models for direct measures of N and SLA, plus partial least squares regression (PLSR) predictions of them (Leaf N-PLSR, SLA-PLSR), totaling four target traits. Three synthetic traits (S1, S2, S3), each a ratio of two wavelengths within the hyperspectral data, were identified based on high co-heritability with target traits. Single-trait (genomic best linear unbiased prediction (GBLUP) served as the baseline model, followed by multi-trait GBLUP models combining synthetic and target traits. Model performance was assessed using fivefold cross-validation under single-trait, CV1, and CV2 schemes. Our approach improves multi-trait genomic prediction of target traits by using synthetic traits with no intrinsic biological meaning selected through co-heritability estimation. This demonstrates that there's more useful information in the spectra than is typically utilized, and this information can be leveraged to improve multi-trait prediction of a target trait.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"139 10","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13588931/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149002463","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Preliminary mapping of wheat (Triticum aestivum L.) tolerance genes to the English grain aphid (Sitobion avenae Fabricius) by genome-wide association study.","authors":"Jie Yang, Jing-Wen Li, Rui Yu, Jing-Feng Peng, Huan-Xing Liu, Long Han, Zhan-Feng Zhang, Yue Song, Xiang-Feng Jing, Xiang-Shun Hu, De-Jun Han, Tong-Xian Liu","doi":"10.1007/s00122-026-05377-5","DOIUrl":"10.1007/s00122-026-05377-5","url":null,"abstract":"<p><strong>Key message: </strong>Six Sitobion avenae-tolerant wheat accessions, mapped 110 associated SNPs and six candidate genes were identified, providing valuable genetic resources for breeding wheat with tolerance to S. avenae. Wheat tolerance to the English grain aphid (Sitobion avenae) is rarely incorporated into integrated pest management strategies for wheat fields. The scarcity of tolerant accession and insufficient mapping of tolerance-related gene are key limiting factors. To address these gaps, 640 wheat accessions were evaluated for S. avenae tolerance, combined with genome-wide association study (GWAS) and qPCR validation. Six wheat accessions with stable tolerance were identified: Lerma Rojo 64, AC Vista, Hanxuan 10, Zimai, Ningnuomai 1, Louguding. A total of 110 single nucleotide polymorphism (SNP) loci associated with tolerance to S. avenae were mapped, and six candidate genes (TraesCS2D03G0041800, TraesCS2Dnew048215, TraesCS2D03G0046300, TraesCS6B03G0655800, TraesCS2Dnew048223, TraesCS2D03G0040800) were examined for transcriptional responses following aphid infestation via qRT-PCR. These genes are involved in cellular redox homeostasis, ADP-binding-mediated defense, and photosystem II (PSII) functionality. This study provides valuable genetic resources for breeding wheat with tolerance to S. avenae and lays a foundation for subsequent functional validation of these tolerance genes and its molecular mechanism exploration.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"139 10","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148983500","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of septoria nodorum blotch susceptibility genes in hard winter wheat.","authors":"Anju Maan Ara, Danielle J Holmes, Timothy L Friesen, Brett F Carver, Guihua Bai, Paul St Amand, Amy Bernado, Rajat Sharma, Meriem Aoun","doi":"10.1007/s00122-026-05359-7","DOIUrl":"10.1007/s00122-026-05359-7","url":null,"abstract":"<p><strong>Key message: </strong>Characterized and unknown septoria nodorum blotch sensitivity/resistance genes were identified in contemporary US hard winter wheat. The necrotrophic fungus Parastagonospora nodorum is the causal agent of septoria nodorum blotch (SNB) of wheat. To determine the prevalence of SNB sensitivity genes in a contemporary US hard winter wheat (HWW), we evaluated a panel of 619 breeding lines and cultivars against five P. nodorum isolates and five necrotrophic effectors (NEs), SnToxA, SnTox1, SnTox3, SnTox267, and SnTox5, and genotyped the panel using genotyping-by-sequencing (GBS) markers and diagnostic kompetetive allele-specific PCR (KASP) markers for the sensitivity genes Tsn1-B1, Snn1-B1, and Snn3-B1/B2. GBS analysis identified 34,357 GBS-single-nucleotide polymorphism (SNP) markers. Evaluations against P. nodorum isolates showed that 40-67% of the genotypes were susceptible in the panel. Toxin infiltration assays showed that 54%, 2%, 37%, 13%, and 15% of the genotypes were sensitive to SnToxA, SnTox1, SnTox3, SnTox267, and SnTox5, respectively. Diagnostic KASP markers for Tsn1-B1, Snn1-B1, and Snn3-B1/B2 showed prediction accuracies of 98%, 75%, and 92% for the corresponding effectors SnToxA, SnTox1, and SnTox3, respectively. Genome-wide association studies (GWAS) not only confirmed the presence of the previously characterized sensitivity genes Tsn1-B1, Snn1-B1, Snn2, Snn3-B1/B2, and Snn5-B1, but also identified new loci to be associated with responses to P. nodorum isolates and NEs. Of these, Qsnb.osu-2AS on chromosome 2AS was associated with responses to all five isolates. KASP markers linked to Snn5-B1, Snn2, and Qsnb.osu-2AS were developed for potential use in marker-assisted selection. These findings should guide breeding for SNB resistance in hard winter wheat.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"139 10","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13578052/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148978084","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}