Theoretical and Applied Genetics最新文献

{"title":"Identification of quantitative trait loci and candidate genes underlying kernel traits of wheat (Triticum aestivum L.) in response to drought stress.","authors":"Jingfu Ma, Tian Tian, Peng Wang, Yuan Liu, Peipei Zhang, Tao Chen, Lijian Guo, Yanyan Zhang, Yuxuan Wu, Fahimeh Shahinnia, Delong Yang","doi":"10.1007/s00122-025-05001-y","DOIUrl":"10.1007/s00122-025-05001-y","url":null,"abstract":"<p><strong>Key message: </strong>Fourteen environmentally stable QTLs for kernel traits were identified and shown to interact significantly with drought-stressed environments. Initial investigation of candidate genes from ten QTL clusters was undertaken, including a KASP marker for TaCYP71E1-A1 on chromosome 5A. Kernel traits, as critical yield components in wheat (Triticum aestivum L.), are governed by quantitative inheritance and are influenced by drought. The identification of quantitative trait loci (QTL) underlying wheat kernel traits in response to drought stress will help enhance breeding for dryland wheat yield. In this study, a hexaploid wheat population of 160 F₈ recombinant inbred lines (RILs) derived from a cross between 'GW011' and 'Jinmai47' and genotyped using the Wheat 90 K Infinium Single Nucleotide Polymorphism (SNP) array were employed to identify QTLs for six kernel traits under drought-stressed and well-watered conditions across six environments. A total of 85 additive QTLs, including 16 for thousand-kernel weight (TKW), 14 for kernel length (KL), 16 for kernel width (KW), 11 for kernel thickness (KT), 18 for kernel size (KS), and 10 for kernel diameter ratio (KDR), were identified with significant additive and QTL × water environmental interaction (QEI) effects. Among them, 14 QTLs were identified as environmentally stable (being identified in five or more test environments), where 12 stable loci were further refined into ten QTL clusters on chromosomes 1B, 2B, 5A, 5B, 5D, 6D, 7A and 7D. A total of 3738 genes were extracted from the confidence intervals of these QTL clusters. A candidate gene, TraesCS5A02G288000 (TaCYP71E1-A1) involved in the cytochrome P450 pathway, was identified within the C3 QTL cluster interval which is associated with KL and KS on chromosome 5A. A Kompetitive Allele Specific PCR (KASP) marker for TaCYP71E1-A1 was developed and validated across 220 wheat varieties. These results provide insight into the genetic basis underlying kernel traits in response to drought stress and will facilitate the genetic improvement of dryland wheat productivity.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 9","pages":"216"},"PeriodicalIF":4.2,"publicationDate":"2025-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144875369","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":"Correction: Non‑additive dosage‑dependent effects of TaGS3 gene editing on grain size and weight in wheat.","authors":"Wei Wang, Qianli Pan, Bin Tian, Zitong Yu, Dwight Davidson, Guihua Bai, Alina Akhunova, Harold Trick, Eduard Akhunov","doi":"10.1007/s00122-025-04998-6","DOIUrl":"10.1007/s00122-025-04998-6","url":null,"abstract":"","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 9","pages":"217"},"PeriodicalIF":4.2,"publicationDate":"2025-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12364759/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144875365","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 mapping and isolation of Rht28, a locus on wheat chromosome arm 2AL affecting plant height, grain size, and grain weight.","authors":"Zhuo Liu, Jiaojiao Zhu, Qiuyue Zhao, Yiwen Cao, Qiuhong Wu, Junru Zhang, Yongxing Chen, Qingpeng Sun, Runzhi Li, Heng Tang, Zhiyong Liu, Jun Han","doi":"10.1007/s00122-025-05006-7","DOIUrl":"10.1007/s00122-025-05006-7","url":null,"abstract":"<p><strong>Key message: </strong>We identified Rht28, a novel dwarf gene on the wheat chromosome arm 2AL, and investigated its effect on important agronomic traits. The genetic dissection of wheat plant height (PH) and the identification of new dwarf or semi-dwarf genes will help breeders to improve yield potential. In this study, QPh-2A.2, a newly discovered locus controlling PH and explaining 7.29%-14.61% of the phenotypic variation across ten environments, was identified using a recombinant inbred line (RIL) population derived from the cross Yanda 1817 × Beinong 6 through a previously constructed single nucleotide polymorphism (SNP) genetic linkage map. To confirm the stability and effect of QPh-2A.2, 22 tightly linked markers were developed based on the released Chinese Spring (CS) reference genome sequence, and a high-density genetic linkage map of the target locus was constructed. QPh-2A.2 is a newly discovered locus controlling PH in wheat, which is temporarily designated Rht28. Additionally, Rht28 was found to have significant effects on thousand-grain weight, grain width, grain thickness, and grain weight per spike, as evaluated in the RIL population, while other agronomic traits related to flag leaf and spike traits were not significantly affected. Moreover, using a large segregating population and extensive progeny tests, we mapped Rht28 within a 3.17-Mb physical region between the markers WBUA4036 and WBUA4413 on the long arm of chromosome 2A. This targeted region contains 51 annotated genes according to CS v2.1 reference genome sequence, and two of these were speculated to be candidates for Rht28. Exploring new dwarf genes is a vital route to breed lodging-resistant wheat cultivars. This study also provides important information for Rht28 marker-assisted selection in wheat breeding programs.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 9","pages":"218"},"PeriodicalIF":4.2,"publicationDate":"2025-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144875367","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":"Fine mapping and prediction of a candidate gene for wrinkled rind in melon (Cucumis melo L.).","authors":"Xufeng Fang, Ziqiao Ji, Min Tao, Xuezheng Wang, Xian Zhang, Zuyun Dai, Zhongzhou Yang, Chaonan Wang, Zicheng Zhu, Shi Liu, Feishi Luan","doi":"10.1007/s00122-025-05014-7","DOIUrl":"10.1007/s00122-025-05014-7","url":null,"abstract":"<p><strong>Key message: </strong>The Cmwr locus was fine mapped to chromosome 2 in wrinkled-rind melon, and MELO3C010304.2 (CmNaa35, encoding an N-α-acetyltransferase) was identified as the most likely candidate gene for wrinkled rind in melon. The wrinkled rind (wr) phenotypic trait in melon is rare, and the regulatory mechanisms and genes governing this feature remain unclear. In this study, genetic analysis of a segregating F₂ population derived from the wrinkled rind melon line T16-085 and the smooth rind line T15-022 suggested that the wr trait is controlled by a single recessive gene, designated Cmwr. Scanning electron microscopy suggested that rind wrinkling is caused by the uneven aggregation of rind cells. Bulked segregant analysis (BSA) delimited the candidate region to approximately 1.90 Mb on chromosome 2, genetic linkage analysis refined this locus to a 448.24-kb region, and fine mapping of data from 1140 F₂ individuals restricted it to a 72.24-kb region containing eight candidate genes. The analysis of sequence variation in coding regions from the parental lines and eight melon germplasms with distinct rind morphologies indicated that MELO3C010304.2 (annotated as an N-α-acetyltransferase, CmNaa35) was the best candidate gene for the Cmwr locus. Two single nucleotide polymorphism (SNP) loci in the coding region (SNP^16,734,095 and SNP^16,734,346) co-segregated with the wr trait. The analysis of promoter cis-acting elements and activity indicated that external indole-3-acetic acid treatment induced CmNaa35 expression. Our findings suggest that Cmwr is responsible for the wr trait in melon and provide genetic resources for further investigation, including gene function analysis and the exploration of the molecular mechanisms underlying melon rind wrinkling.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 9","pages":"215"},"PeriodicalIF":4.2,"publicationDate":"2025-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144875366","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":"Genome-wide association study reveals novel SNP loci and candidate genes linked to flowering time in upland cotton.","authors":"Xuefeng Guo, Junning Yang, Dandan Li, Xueli Zhang, Wenmin Yuan, Ying Li, Fuxiang Wang, Qi Ma, Caixiang Wang, Junji Su","doi":"10.1007/s00122-025-05011-w","DOIUrl":"10.1007/s00122-025-05011-w","url":null,"abstract":"<p><strong>Key message: </strong>A total of 456 SNPs associated significantly with FT via GWAS and three candidate genes related to flowering were identified via RNA‒seq, qRT‒PCR and VIGS. Flowering time (FT) is one of the main traits associated with early maturity in upland cotton; however, genetic basis and candidate genes underlying FT remain inadequately understood. In this study, 1,574,032 high-quality single nucleotide polymorphisms (SNPs) were identified on the basis of resequencing data from 619 upland cotton lines, and among them, 418 core germplasms were selected and genome-wide association studies (GWASs) were conducted to identify 456 SNPs that were significantly associated with FT. Variant annotation of significant SNPs revealed that 25 of these SNPs resulted in nonsynonymous mutations in eight genes. Three early-flowering-favouring haplotypes (A02_Hap3, D10_Hap3 and D11_Hap3) and two early-flowering-favouring alleles (D09_6523710_GG and D09_50028094_AA) were identified by haplotype/allele analysis. By RNA‒seq and qRT‒PCR, three candidate genes (GhFRO7, GhCML1 and GhPCMP-E88) were also shown to be differentially expressed between early-flowering and late-flowering varieties. Virus-induced gene silencing (VIGS) experiments further verified the critical roles of the three genes, which were important regulators underlying the late-flowering phenotype in upland cotton, in the regulation of FT. Moreover, selection pressure analysis revealed that these three candidate genes might have experienced artificial or natural selection. In addition, we developed two cleaved amplified polymorphic sequence (CAPS) markers, which have potential application value. These findings will provide a new theoretical basis for the genetic improvement of early maturity-related traits in upland cotton and lay the foundation for the breeding of excellent early maturing varieties.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 9","pages":"214"},"PeriodicalIF":4.2,"publicationDate":"2025-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144875368","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":"Phenotypic characterization and genetic factor identification of starch content-related traits in foxtail millet (Setaria italica L.).","authors":"Shaohua Chai, Yan Guo, Zhixiu Ma, Yongjiang Wu, Yujie Li, Chuanxing Wang, Yajun Li, Jinfeng Gao, Hongqi Chen, Hui Song, Baili Feng, Pu Yang","doi":"10.1007/s00122-025-05012-9","DOIUrl":"10.1007/s00122-025-05012-9","url":null,"abstract":"<p><strong>Key message: </strong>Twenty-two QTL controlling starch synthesis were identified in foxtail millet, and 14 potential candidate genes were predicted. The content of starch, including amylose and amylopectin, is an essential trait for foxtail millet quality, but its complexity and genetic basis are still poorly understood. Here, a recombinant inbred line (RIL) population, comprising 215 foxtail millet lines, was employed to analyze the variation in three starch content-related traits and to identify the associated quantitative trait loci (QTL) in six environments. We found abundant phenotypic variation and very high heritability (86.52-97.77%) for three starch content-related traits among the RIL population. The QTL mapping identified 22 QTL, 36 combined QTL, and 55 epistatic QTL pairs for starch content-related traits. Of these, 17 QTL were identified in two to six environments, and three co-located QTL clusters were revealed, including the triple QTL cluster qC4.1, which was detected 16 times in six environments. The pathway-driven analysis revealed 14 candidate genes, one of which is Seita.4G022400, which encodes a granule-bound starch synthase in the starch and sucrose metabolism pathway, as the causal gene for the QTL cluster qC4.1. Using phenotypic and genotype data of 224 foxtail millet accessions, we conducted haplotype analysis for Seita.4G022400, which showed high correlations with amylose content, suggesting potential applications for Seita.4G022400 in foxtail millet starch and yield improvement. Additionally, the haplotype analysis identified five other genes (Seita.2G114900, Seita.3G209500, Seita.5G419900, Seita.2G137100, and Seita.3G011400) that exhibit high correlations with three starch content-related traits. Our results provide a foundation for further fine mapping and molecular cloning of starch content-related traits in foxtail millet.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 9","pages":"213"},"PeriodicalIF":4.2,"publicationDate":"2025-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144859641","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":"Deciphering the regulatory network of carbon isotope discrimination in bread wheat through genome-wide association studies and genomic prediction.","authors":"Qingfeng Dong, Shan Lu, Hao Ren, Dezheng Liu, Shen-Ao Gao, Xuefen Cai, Shanshan Zhang, Muhammad Ateeq, Liang Chen, Yin-Gang Hu","doi":"10.1007/s00122-025-04980-2","DOIUrl":"10.1007/s00122-025-04980-2","url":null,"abstract":"<p><strong>Key message: </strong>A total of 125 QTL regions and 33 candidate genes associated with carbon isotope discrimination (CID) were identified in wheat, and genomic prediction (GP) achieved high accuracy (Pearson correlation coefficient, PCC = 0.665), providing valuable tools for reeding drought-resilient varieties. Carbon isotope discrimination (CID) is a critical physiological trait that serves as an indicator of water use efficiency (WUE) and drought tolerance in wheat. In this study, the genetic basis of CID was analyzed through genome-wide association studies (GWAS) and genomic prediction (GP) using a diverse panel of 238 wheat varieties. High-density genotyping identified 125 significant quantitative trait loci (QTL) regions and 33 candidate genes, primarily involved in stomatal regulation, drought tolerance, chloroplast development, chlorophyll metabolism, leaf development, and light signaling pathways. Bayesian ridge regression was used to predict CID under normal water (CID_NW), water-limited (CID_WL), rain-fed conditions (CID_RF), and a combined environment (CID_BLUE). The model showed stable performance across environments, with the highest accuracy (Pearson correlation coefficient, PCC = 0.665 for CID_RF) achieved using a genotype matrix containing the SNP with the lowest p-value from each QTL. These findings provide novel insights into the genetic architecture of CID and its potential role in enhancing drought tolerance in wheat. The identified QTL, candidate genes, and predictive models offer a strong foundation for marker-assisted selection (MAS) and genome-wide selection (GS) in wheat breeding programs. These results contribute to the development of drought-resilient wheat varieties, addressing key challenges in global wheat production and food security.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 9","pages":"212"},"PeriodicalIF":4.2,"publicationDate":"2025-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144837790","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":"Effects of using deep learning to predict the geographic origin of barley genebank accessions on genome-environment association studies.","authors":"Che-Wei Chang, Karl Schmid","doi":"10.1007/s00122-025-05003-w","DOIUrl":"10.1007/s00122-025-05003-w","url":null,"abstract":"<p><p>Genome-environment association (GEA) is an approach for identifying adaptive loci by combining genetic variation with environmental parameters, offering potential for improving crop resilience. However, its application to genebank accessions is limited by missing geographic origin data. To address this limitation, we explored the use of neural networks to predict the geographic origins of barley accessions and integrate imputed environmental data into GEA. Neural networks demonstrated high accuracy in cross-validation but occasionally produced ecologically implausible predictions as models solely considered geographical proximity. For example, some predicted origins were located within non-arable regions, such as the Mediterranean Sea. Using barley flowering time genes as benchmarks, GEA integrating imputed environmental data ( <math><mrow><mi>N</mi> <mo>=</mo> <mn>11</mn> <mo>,</mo> <mn>032</mn></mrow> </math> ) displayed partially concordant yet complementary detection of genomic regions near flowering time genes compared to regular GEA ( <math><mrow><mi>N</mi> <mo>=</mo> <mn>1</mn> <mo>,</mo> <mn>626</mn></mrow> </math> ), highlighting the potential of GEA with imputed data to complement regular GEA in uncovering novel adaptive loci. Also, contrary to our initial hypothesis anticipating a significant improvement in GEA performance by increasing sample size, our simulations yield unexpected insights. Our study suggests potential limitations in the sensitivity of GEA approaches to the considerable expansion in sample size achieved through predicting missing geographical data. Overall, our study provides insights into leveraging incomplete geographical origin data by integrating deep learning with GEA. Our findings indicate the need for further development of GEA approaches to optimize the use of imputed environmental data, such as incorporating regional GEA patterns instead of solely focusing on global associations between allele frequencies and environmental gradients across large-scale landscapes.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 9","pages":"211"},"PeriodicalIF":4.2,"publicationDate":"2025-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12343745/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144822602","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":"CRISPR/Cas system-mediated transgene-free or DNA-free genome editing in plants.","authors":"Rongxiao Cai, Nan Chai, Jiekun Zhang, Jiantao Tan, Yao-Guang Liu, Qinlong Zhu, Dongchang Zeng","doi":"10.1007/s00122-025-04990-0","DOIUrl":"https://doi.org/10.1007/s00122-025-04990-0","url":null,"abstract":"<p><p>CRISPR/Cas-based genome-editing technology serves as a powerful and versatile tool for genome modification. It has been broadly utilized in crop breeding to enhance traits such as yield, various quality attributes, and biotic and abiotic stress tolerance. Because of public safety concerns over genetically modified organisms (GMOs), many countries have established stringent regulatory policies for genetically modified plants, dramatically limiting the application of related products. However, genome editing in stably transformed plants can result in transgene-free progeny through self-pollination or hybridization or yield DNA-free gene-edited plants via transient transformation. These edited plants materially differ from GMOs and are referred to as genome-edited organisms (GEOs). GEOs have the potential to alleviate regulatory burdens and aid in commercialization. Various methods have been developed to expedite the creation of transgene-free or DNA-free GEOs. This review summarizes the various strategies for creating these types of GEOs based on the CRISPR/Cas systems. It also covers the advantages and drawbacks of these strategies. Additionally, we examine off-target effects and mitigation strategies for plant genome editing and outline regulatory policies for gene-edited crops in selected countries and regions. We hope this review offers valuable references for the advancement of transgene-free and DNA-free GEOs.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 9","pages":"210"},"PeriodicalIF":4.2,"publicationDate":"2025-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144822601","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":"Integrated transcriptome and BSA-seq analysis identifies a novel QTL for Meloidogyne graminicola resistance in rice HuaHang31.","authors":"Zhuhong Yang, Qingyan Xiao, Yao Wang, Yingjun Zhang, Shan Ye, Pingyong Sun, Wuhan Zhang, Huafeng Deng, Shiming Liu, Zhong Ding","doi":"10.1007/s00122-025-04999-5","DOIUrl":"https://doi.org/10.1007/s00122-025-04999-5","url":null,"abstract":"<p><strong>Key message: </strong>A novel QTL on chromosome 11 with 7 candidate genes regulating nematode resistance was identified by RNA-seq-based transcriptome and BSA-seq combination analyses, revealing the possible interactions between nematodes and plants. The resistant rice germplasms against Meloidogyne graminicola, which is a plant-parasitic nematode posing a significant threat to rice production, are very limited. Here, we identified HuaHang31 (HH31), an indica rice variety, as a novel source of high resistance against to M. graminicola through large-scale screening of 297 rice accessions using PF-127 assays. Histopathological and histochemical analyses revealed that HH31 significantly reduced nematode penetration, delayed juvenile development, and triggered reactive oxygen species accumulation and hypersensitive response in root tip cells post-infection. RNA-seq-based transcriptome profiling of HH31 and susceptible IR64 roots at 3-, 7-, and 12-days post-inoculation (dpi) highlighted the up-regulation of phenylpropanoid, flavonoid, lignin biosynthesis, and phytohormone signaling pathways (jasmonic acid, salicylic acid, ethylene) in HH31, suggesting their pivotal roles in nematode resistance. Additionally, bulk segregant analysis of two F₂ populations derived from HH31 crosses with susceptible varieties mapped a novel quantitative trait locus (QTL) on chromosome 11 (4.7-8.2 Mb). Within this region, seven nonsynonymous nucleotide-binding site-leucine-rich repeat genes exhibited root-specific expression and responsiveness to nematode infection, implicating their roles in resistance. Importantly, this QTL represents a distinct genomic region compared to previously reported resistance loci, highlighting its novelty. This study provides a new understanding of the genetic basis of nematode resistance and a valuable source for the development of nematode-resistant rice varieties, offering a sustainable strategy to mitigate yield losses caused by this pervasive pathogen.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 9","pages":"208"},"PeriodicalIF":4.2,"publicationDate":"2025-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144817549","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}