Theoretical and Applied Genetics最新文献

{"title":"Alternative splicing-mediated regulation of a novel allele of Badh2 drives moderate accumulation of 2-AP in rice.","authors":"Xueyu Liang, Ying Chen, Kai Liu, Min Guo, Danhua Zhou, Cuihong Huang, Tao Guo, Hui Wang, Guili Yang","doi":"10.1007/s00122-025-04979-9","DOIUrl":"10.1007/s00122-025-04979-9","url":null,"abstract":"<p><strong>Key message: </strong>A novel allele of Badh2, badh2-I11 undergoes alternative splicing and leads to reduced Badh2 expression and enhanced 2-AP accumulation in rice. Aroma is a crucial quality trait in rice and is primarily regulated by the Badh2 gene located on chromosome 8. In this study, we identified a novel allele of Badh2, badh2-I11, in the aromatic rice variety, Hei126 (H126). This allele harbors a 55-bp deletion in intron 11, inducing alternative splicing, that generates both wild-type transcripts and aberrant transcripts containing a premature stop codon. Consequently, Badh2 mRNA levels are reduced, leading to moderate accumulation of the aromatic compound 2-acetyl-1-pyrroline (2-AP). Genetic analysis of an F₂ population derived from a cross between Huahang 48 (non-aromatic, Badh2/Badh2) and H126 (aromatic, badh2-I11/badh2-I11) revealed a genotypic segregation ratio 1:2:1 (Badh2/Badh2: Badh2/badh2-I11: badh2-I11/badh2-I11), consistent with Mendelian inheritance for a single codominant locus. The corresponding phenotypic ratio of non-aromatic to aromatic plants was 3:1. We developed a codominant InDel marker for efficient screening of badh2-I11 in breeding populations. This intermediate aromatic phenotype establishes H126 as a unique germplasm resource, accumulating 2-AP while retaining partial Badh2 function. Our findings elucidate a novel molecular mechanism of aroma production mediated by intronic alternative splicing and provide valuable genetic resources and molecular tools for aromatic rice breeding.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 8","pages":"194"},"PeriodicalIF":4.2,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144765559","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":"In silico prediction of variant effects: promises and limitations for precision plant breeding.","authors":"Janek Sendrowski, Thomas Bataillon, Guillaume P Ramstein","doi":"10.1007/s00122-025-04973-1","DOIUrl":"10.1007/s00122-025-04973-1","url":null,"abstract":"<p><strong>Key message: </strong>Sequence-based AI models show great potential for prediction of variant effects at high resolution, but their practical value in plant breeding remains to be confirmed through rigorous validation studies. Plant breeding has traditionally relied on phenotyping to select individuals with desirable traits-a process that is both costly and time-consuming. Increasingly, breeding strategies are shifting toward precision breeding, where causal variants are directly targeted based on their effects. To predict the effects of causal variants, in silico methods are emerging as efficient alternatives or complements to mutagenesis screens. Here, we review state-of-the-art machine learning methods for predicting variant effects in plants across both coding and noncoding regions, contrasting supervised approaches in functional genomics with unsupervised methods in comparative genomics. We discuss challenges in validating predictions, and compare these methods with traditional association and comparative genomics techniques. We argue that modern sequence models extend traditional methods by generalizing across genomic contexts, fitting a unified model across loci rather than a separate model for each locus. In doing so, they address inherent limitations of traditional quantitative and evolutionary comparative genetics techniques. However, the accuracy and generalizability of sequence models heavily depend on the training data, highlighting the need for validation experiments. We point to successful applications of sequence models, especially with protein sequences, and identify areas for further improvement, especially in modeling regulatory sequences. While not yet mature for in silico-driven precision breeding, sequence models show strong potential to become an integral part of the breeder's toolbox.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 8","pages":"193"},"PeriodicalIF":4.2,"publicationDate":"2025-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12304032/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144733403","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":"Mapping QTLs for adult-plant resistance to yellow rust in a hard winter wheat population Heyne × Lakin.","authors":"Chunlian Li, Xiao-Ting Xu, Yibo Zhang, Shengjie Liu, Jianhui Wu, Dejun Han, Robert Bowden, John Fellers, Guihua Bai","doi":"10.1007/s00122-025-04971-3","DOIUrl":"10.1007/s00122-025-04971-3","url":null,"abstract":"<p><p>Adult-plant resistance to yellow rust, caused by Puccinia striiformis f. sp. tritici, is a durable type of resistance in wheat (Triticum aestivum L.). To map the quantitative trait loci (QTLs) for adult-plant resistance, 145 (Heyne × Lakin)F_6:7 recombinant inbred lines (RILs) were evaluated for rust infection type (IT) and maximum rust severity (MRS) in multiple environments and genotyped using single-nucleotide polymorphisms (SNPs) derived from 9 K SNP chips and simple sequence repeat markers. Four major QTLs on chromosome arms 2AS (QYr.hwwgr-2AS), 2AL (QYr.hwwgr-2AL), 2BL (QYr.hwwgr-2BL) and 3BS (QYr.hwwgr-3BS) were identified for adult-plant resistance in multiple environments with their resistance alleles all from Heyne, except for QYr.hwwgr-3BS. QYr.hwwgr-2AS and QYr.hwwgr-2BL were significant for both IT and MRS. QYr.hwwgr-2AS showed the largest effect, explaining 10.6-51.3% of the phenotypic variance for MRS in four environments and 31.0% phenotypic variance for low IT in one experiment. QYr.hwwgr-2BL might be a new QTL in a 0.7-cM interval and explained 7.5-22.1% of the phenotypic variance of IT and 10.3-19.0% of the phenotypic variance of MRS. QYr.hwwgr-2AL was mapped at a 3.4-cM interval and explained 4.2-10.7% of the phenotypic variance for IT. QYr.hwwgr-3BS was identified at a 0.7-cM interval, accounting for 5.5-13.6% of the phenotypic variance for IT. Stacking all four QTLs in a single RIL can achieve a low IT of 0-2, which is significantly lower than the resistant parent Heyne.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 8","pages":"192"},"PeriodicalIF":4.2,"publicationDate":"2025-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144733404","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":"Integrating genome assembly, structural variation map construction and GWAS reveal the impact of SVs on agronomic traits of Brassica napus.","authors":"Nian Wang, Xianshuai Song, Lieqiong Kuang, Ze Tian, Kaifeng Wang, Keqi Li, Lan Ge, Yu Wu, Xinfa Wang, Xiaoling Dun, Hanzhong Wang","doi":"10.1007/s00122-025-04977-x","DOIUrl":"10.1007/s00122-025-04977-x","url":null,"abstract":"<p><strong>Key message: </strong>An SV map of B. napus was constructed, SVs association with four agronomic traits were identified. This study provides a more systematic insight into the genetic variation of rapeseed. Rapeseed (Brassica napus L.) is one of the most major oil crops. The rapeseed genome is rich in structural variation (SV), while the functional identification and utilization of SVs are currently limited. In this study, genomes of two rapeseed accessions (4D122 and 5DH2900) were assembled, and the quality of both genomes has been improved compared to the most commonly used rapeseed reference genome ZS11. Using the long-reads sequencing data of 25 representative rapeseed accessions, an SV-map of B. napus was constructed, which contained the position and sequence information of 183,723 SVs; and combining with the long-reads data of 18 B. rapa and 26 B. oleracea accessions, an SV-map of A subgenome and C subgenome of Brassica was also constructed. Based on the SV-map, an SV-set containing 350 rapeseed accessions was constructed using resequencing data with an average sequencing depth of 25 × . SV-GWAS and SNP-GWAS revealed loci that associated with four agronomic traits of rapeseed, including glucosinolate concentrations in seeds (SGC), silique length, leaf trichomes and purple stem. Some potentially causal SVs were identified, such as SVs introduced from B. oleracea was found to may result in purple stem in rapeseed. Overall, this study provided abundant genomic resources for rapeseed, and systematically identified SVs in rapeseed genome and revealed their association with agronomic traits, lay the foundation for revealing the functions and breeding potential of SVs.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 8","pages":"191"},"PeriodicalIF":4.2,"publicationDate":"2025-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144718727","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 a QTL region for tomato brown rugose fruit virus resistance in Solanum pimpinellifolium.","authors":"Namrata Jaiswal, Bazgha Zia, Bidisha Chanda, Andrea Gilliard, Ainong Shi, Kai-Shu Ling","doi":"10.1007/s00122-025-04974-0","DOIUrl":"10.1007/s00122-025-04974-0","url":null,"abstract":"<p><p>Tomato (Solanum lycopersicum L.), one of the most widely grown vegetables in the world, has been seriously impacted in the past decade by the emerging tomato brown rugose fruit virus (ToBRFV). ToBRFV is a seed-borne tobamovirus, with ability to overcome the commonly used Tm-2² resistance gene in tomato. The objective of this study was to conduct quantitative trait locus (QTL) mapping and identify single-nucleotide polymorphism (SNP) markers associated with ToBRFV resistance in tomato. Two F₂ populations were used for QTL mapping: One derived from a cross between S. pimpinellifolium USVL333 (PI 390718) × USVL332 (PI 390717) and another from 'Moneymaker' × USVL332 (PI 390717), with population sizes of 195 and 79 plants, respectively. The resistance trait was derived from the S. pimpinellifolium accession USVL332 (PI 390717). A major QTL for ToBRFV resistance was identified on chromosome 11 (SL4.0ch11), with the peak located at approximately 46.84 Mbp. This QTL spans a 22-kb interval between 46,825,788 bp and 46,847,421 bp, as determined through both genome-wide association study (GWAS) and QTL linkage mapping. Three SNP markers, SL4.0ch11_46825788, SL4.0ch11_46847421, and SL4.0ch11_46850215, demonstrated the most significant association with high LOD values (LOD = 13 in the Blink model) in GWAS analysis. In this genomic region, two disease resistance gene analogs, Solyc11g062150 (TIR-NBS-LRR resistance protein, Toll-Interleukin receptor) and Solyc11g062180 (disease resistance protein, leucine-rich repeat), were identified, which may serve as candidates for ToBRFV resistance. The QTL identified in this study could be valuable for plant breeders in facilitating tomato breeding with ToBRFV resistance.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 8","pages":"190"},"PeriodicalIF":4.2,"publicationDate":"2025-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12283848/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144691626","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":"Genotyping by target sequencing (GBTS)-based genetic mapping uncovers synergistic interactions for stripe rust resistance in wheat cultivar Flanders.","authors":"Lei Liu, Jinyu Han, Dandan Zhang, Yuqing Li, Chuanliang Zhang, Shengjie Liu, Ziyi Yan, Weijun Zheng, Chunlian Li, Qingdong Zeng, Zhensheng Kang, Dejun Han, Wentao Zhang, Qiang Yao, Jianhui Wu","doi":"10.1007/s00122-025-04969-x","DOIUrl":"10.1007/s00122-025-04969-x","url":null,"abstract":"<p><strong>Key message: </strong>YrFLA.1, YrFLA.2 and YrFLA.3, identified in wheat cultivar Flanders, collaboratively boost the level of adult plant resistance to stripe rust. Bread wheat cultivar Flanders has maintained an adequate level of adult plant resistance (APR) to stripe rust in China for more than 30 years despite exposure to a changing and variable pathogen population. To identify genomic segments conferring stripe rust resistance, an F_2:7 recombinant inbred line (RILs) population from a cross of Avocet S and Flanders was analyzed genetically. The population and parents were evaluated in multiple environments and genotyped using the GenoBaits^®WheatSNP16K array. Three stable QTL detected on chromosome arms 1BL, 3BL and 7BL were designated QYrfla.nwafu-1BL.7 (YrFLA.1, in a hot-spot region), QYrfla.nwafu-3BL.2 (YrFLA.2, possibly novel) and QYrfla.nwafu-7BL.6 (YrFLA.3, in a hot-spot region), respectively. YrFLA.3 was more effective than YrFLA.1 and YrFLA.2 in all environments, but synergistic interaction between all three loci led to significant enhancement of resistance. Under rust-free conditions there was almost no difference in thousand grain weight, but results from the rust nursery indicated a 21.81-28.76% reduction in the RILs lacking the QTL compared to the RILs with one or more QTL. On the other side, a panel of 679 current Chinese cultivars and breeding lines based on the GenoBaits assay was used to characterize the haplotype variation and the distribution of these loci. The haplotypes with the YrFLA.1, YrFLA.2 and YrFLA.3 regions have frequencies of 65.83, 18.99 and 43.44%, respectively, reducing disease severities of 17.57-37.54%. These findings indicate that effective gene pyramiding strategy is crucial for developing high yielding and durable resistance cultivars.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 8","pages":"187"},"PeriodicalIF":4.2,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144675625","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":"A high-throughput pipeline for phenotyping, object detection and quantification of leaf trichomes.","authors":"Andrea González-Muñoz, Dai-Jie Wu, Ana B Perera-Rodríguez, Mohamed Rekik, Silvio Giancola, Brande B H Wulff, Catherine Gardener","doi":"10.1007/s00122-025-04967-z","DOIUrl":"10.1007/s00122-025-04967-z","url":null,"abstract":"<p><strong>Key message: </strong>We developed a new high-throughput device and AI image detection model capable of rapidly collecting phenotype data for a population of wild grass, facilitating identification of genomic regions associated with trichome density. Access to increasing amounts of high-quality genomic sequence data for many plant species is allowing for faster, more accurate gene identification. To maximize the use of this sequence data for association genetics, gene discovery, and validation, it must be coupled with phenotype data. However, phenotype data acquisition can represent a bottleneck in studies requiring many datapoints, such as large diversity panels for genome-wide association studies. Here we developed a portable handheld imaging device-the Tricocam-and method for image capture and semi-automated quantification of leaf edge trichomes in a grass species. Trichomes have been implicated in abiotic and biotic stress tolerance in grasses, but so far, no trichome genes have been cloned in this plant family. We also refined and implemented the AI detection processes underpinning the web-based image quantification platform from Thya Technology® to rapidly quantify leaf edge trichomes. We used the phenotype acquisition method in the wild wheat progenitor Aegilops tauschii in combination with k-mer-based Genome-Wide Association Study to validate a trichome-controlling genomic region on chromosome arm 4DL and discover a new one on 4DS. By making the Tricocam 3D print design and AI visual detection model public, we aim to deliver useful resources for the plant science community to use or adapt for other large-scale phenotyping projects on diversity panels.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 8","pages":"188"},"PeriodicalIF":4.2,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12279567/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144683227","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":"QTL mapping and underlying genes for heat tolerance in grapevine (Rhine Riesling × Cabernet Sauvignon) under field conditions.","authors":"Silvia Pettenuzzo, Luca Cappellin, Michele Faralli, Maria Stella Grando, Laura Costantini","doi":"10.1007/s00122-025-04972-2","DOIUrl":"10.1007/s00122-025-04972-2","url":null,"abstract":"<p><strong>Key message: </strong>QTL analysis for key physiological traits assessed during hot days highlighted 26 genomic regions and promising candidate genes for thermotolerance and response to light stress under field conditions in grapevine. Grapevine is one of the most widely cultivated perennial fruit crops in the world, with its economic relevance mainly related to wine production. Climate change, with global warming and increased frequency of intense phenomena, is greatly affecting viticulture and the wine sector. Thus, studying the genetic factors involved in grapevine response to high temperatures can help to improve vineyard management strategies and support plant breeding innovations. In this experiment, a mapping population (Rhine Riesling × Cabernet Sauvignon) was used to perform a genetic dissection of the physiological response to increased temperatures under vineyard conditions. Photosynthetic activity and stomatal dynamics were evaluated for three seasons during hot days at different plant developmental stages. Results of quantitative trait loci (QTL) analysis highlighted 26 genomic regions that consistently contribute to the eight tested traits. Candidate genes with supporting evidence, underlying QTL clusters with explained variance above 10%, are those associated with signal perception and transduction, protein homeostasis, osmoprotection, photosynthesis and response to radiation which are relevant mechanisms for plant heat acclimation. Within the stable chromosomal intervals identified by this exploratory analysis, other gene predictions emerged that may be tested for their involvement in grapevine resilience to increasing temperatures. The genetic architecture of quantitative traits linked to grapevine heat tolerance investigated under real field conditions, helps to define key targets for adapting an important traditional crop to environmental changes.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 8","pages":"189"},"PeriodicalIF":4.2,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12279613/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144683228","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":"The combination of linkage mapping, genome-wide association study, and dynamic transcriptome analysis reveals conserved candidate genes for salt tolerance in maize.","authors":"Ziyi Xiao, Zhenyuan Pan, Xinxin Liu, Xueqing Zheng, Guantao Wang, Yayu Fu, Mengmeng Li, Bin Hou, Xuhua Li, Ming Zhang, Chunlan Jia, Fazhan Qiu","doi":"10.1007/s00122-025-04975-z","DOIUrl":"10.1007/s00122-025-04975-z","url":null,"abstract":"<p><strong>Key message: </strong>Six candidate genes for salt tolerance were identified through a accumulation of QTL mapping, GWAS, and transcriptome analysis. Additionally, the accumulation of favorable alleles significantly improved salt tolerance. Salinization in China is primarily concentrated in the northeast, northwest, and north regions, which overlap heavily with maize-growing areas, severely affecting maize production. Therefore, it is essential to uncover the genetic basis of salt tolerance and enhance maize's salt tolerance. In this study, we evaluated the survival rates of a BC₂F₇ population and a natural population under salt stress across three environments, revealing significant variation among the accessions. We then performed quantitative trait loci (QTL) mapping and genome-wide association study (GWAS) using genotyping data from 11,312 single nucleotide polymorphisms (SNPs) in the BC₂F₇ and 3,619,762 SNPs in the natural population. As a result, we identified three QTLs and 187 significant SNPs, including one QTL and 19 SNPs consistently detected across multiple environments. To identify candidate genes, we integrated QTL mapping, GWAS results, and dynamic transcriptome analysis under salt treatment. Six candidate genes were identified as potential contributors to salt tolerance. Furthermore, though the favorable alleles of the candidate genes can improve the salt tolerance in maize, there are relatively few germplasm in the natural population that simultaneously possess multiple favorable alleles. In the future, molecular marker-assisted selection could be employed to introgress these favorable alleles into elite lines to enhance their salt tolerance. This study has expanded the understanding of the genetic basis underlying salt tolerance in maize at the seedling stage, providing critical molecular targets for salt tolerance in maize, which facilitates yield increase in saline-alkali soils.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 8","pages":"186"},"PeriodicalIF":4.2,"publicationDate":"2025-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144668566","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 a stable genetic locus and candidate genes for Fusarium head blight resistance on wheat chromosome 3BL.","authors":"Qiang Ning, Qing Xu, Derong Gao, Yuanfeng Hao, Yong Zhang, Ling Chen, Yide Liu, Hanwen Tong, Yuqing Zhang, Zhanwang Zhu, Yike Liu","doi":"10.1007/s00122-025-04970-4","DOIUrl":"10.1007/s00122-025-04970-4","url":null,"abstract":"<p><p>Fusarium head blight (FHB) is a devastating wheat disease worldwide. Identifying novel quantitative trait loci (QTLs) and resistance-associated genes is critical for breeding resistant cultivars. In this study, we conducted a comprehensive genetic analysis of FHB resistance in a diverse panel of 240 wheat accessions phenotyped over three years. Genome-wide association studies (GWAS) revealed 57 significant SNPs, delineating five stable QTLs on chromosomes 3B, 4A, 7A, and 7D that collectively explained 4.8-7.0% of phenotypic variation. Notably, qFHB3B.1 co-localized with the known Fhb1 locus, the other four QTLs represent novel genomic regions. Allelic stacking analysis demonstrated a strong correlation (R² = 0.96), with accessions carrying four favorable alleles showing a 44.7% reduction in FHB index compared to null allele. Furthermore, we developed and validated a kompetitive allele specific PCR marker for a leading SNP within qFHB3B.2, confirming its stable effects across 132 wheat accessions and two doubled haploid population. Comparative transcriptomic analysis of resistant and susceptible genotypes identified 4,302 consistently differentially expressed genes. Nine high-confidence candidate genes showing both GWAS signals and differential expression were prioritized, including TraesCS3B02G359600 and TraesCS3B02G359800 within qFHB3B.2,which exhibited contrasting expression patterns suggesting opposing roles in FHB resistance. Our findings provide valuable insights into the genetic architecture of FHB resistance and identify promising targets for marker-assisted breeding in wheat.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 8","pages":"185"},"PeriodicalIF":4.2,"publicationDate":"2025-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144668565","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}