Theoretical and Applied Genetics最新文献

{"title":"Mining QTLs and candidate genes in bread wheat associated with kernel hardness through GWAS.","authors":"Qinglin Wen, Dezheng Liu, Shan Lu, Xue Wang, Linzhou Huang, Liang Chen, Yin-Gang Hu","doi":"10.1007/s00122-026-05254-1","DOIUrl":"https://doi.org/10.1007/s00122-026-05254-1","url":null,"abstract":"<p><strong>Key message: </strong>35 candidate quantitative trait loci (QTLs) and 12 key candidate genes have been identified as associated with kernel hardness in wheat. They encode γ-gliadins, Avenin-3, glutenin subunits, β-glucosidase, α-galactosidase, 1,4-α-glucan-branching enzyme. Kernel hardness constitutes a core indicator of wheat quality, reflecting endosperm texture characteristics and playing a decisive role in milling performance. This study employed 189 genetically diverse bread wheat accessions, integrating genome-wide association studies (GWAS) with genomic prediction techniques to elucidate the genetic mechanisms underlying kernel hardness. Kernel hardness index (KHI) exhibited significant phenotypic variation across four environments and best linear unbiased estimation (BLUE) values within the test population. GWAS conducted using wheat 660 K SNP chip genotyping data identified 67 quantitative trait locis (QTLs) consistently associated with KHI in at least two environments (includes BLUE values). Among these, 35 QTLs showed significant KHI differences across environments based on their different haplotypes. Functional annotation of genes within QTL regions identified 12 key candidate genes encoding γ-amylopectin, Avenin-3, glutenin sub-units, β-glucosidase, α-galactosidase, 1,4-α-glucan-branching enzyme, which are presumed to be closely associated with KHI. Genomic prediction using Bayesian ridge regression achieved over 75% accuracy across all three SNP matrices. These findings provide theoretical and technical support for understanding the genetic basis of wheat KHI and for screening innovative wheat germplasm resources with distinct kernel hardness.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"139 6","pages":""},"PeriodicalIF":4.2,"publicationDate":"2026-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147843173","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":"The genetic and developmental enigma of rhizomes: crucial traits with limited understanding.","authors":"Hongfei Chen, Jenn M Coughlan","doi":"10.1007/s00122-026-05229-2","DOIUrl":"https://doi.org/10.1007/s00122-026-05229-2","url":null,"abstract":"<p><p>Rhizomes, horizontal underground stems, play fundamental roles in plant persistence and perennial growth by enabling clonal propagation, resource storage, and stress resilience. Despite their ecological and agronomic importance across plant lineages, the genetic and developmental regulation of rhizomes remains poorly characterized. Here, we synthesize findings from in vitro induction studies, in vivo developmental analyses, quantitative trait loci (QTL) mapping, comparative transcriptomics, and limited functional studies to evaluate current knowledge and highlight outstanding questions in rhizome biology. Results from both in vitro and whole-plant studies show that phytohormones, particularly auxin, cytokinin, and gibberellin, are central regulators of rhizome initiation and growth, with effects mediated in a context-dependent manner through interactions with environmental and developmental cues. Across rhizomatous species, traits such as rhizome initiation, branching, and elongation are often polygenic, although comparatively simpler genetic architectures associated with repeated rhizome evolution have been documented in emerging model systems like Mimulus. Transcriptomic analyses further highlight hormone signaling, stress response, and carbohydrate metabolism pathways as key regulatory components. However, few genes have been functionally validated, underscoring the need for tractable systems for genetic dissection. Perennial Mimulus species are proposed as promising models for rhizome research due to their experimental accessibility, ecological relevance, and established genomic resources. Integrated approaches leveraging fine-mapping, near-isogenic lines, multi-omics, and gene editing are poised to accelerate discovery of causal loci and regulatory networks underlying rhizome development, thereby clarifying the genetic and developmental bases of rhizome traits underlying their repeated evolution, with broader implications for perenniality, environmental responses, and crop improvement.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"139 6","pages":""},"PeriodicalIF":4.2,"publicationDate":"2026-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147843148","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":"Widespread non-target-site resistance in Setaria viridis to four classes of herbicide.","authors":"Thomas H Pendergast, Sailaja Maddali, Srinivasa R Chaluvadi, Peng Qi, William K Vencill, Jeffrey L Bennetzen, Katrien M Devos","doi":"10.1007/s00122-026-05240-7","DOIUrl":"https://doi.org/10.1007/s00122-026-05240-7","url":null,"abstract":"<p><strong>Key message: </strong>Although herbicide resistance in Setaria is rampant and cosmopolitian across four herbicide families, we encountered little evidence of target-site resistance, indicating diverse non-target mechanisms of metabolizing, sequestering, and overwhelming herbicides. Setaria viridis is a cosmopolitan weed and model genetic system with increasing reports of resistance to multiple classes of herbicides. Our goal was to assess the herbicide resistance and allelic diversity in herbicide target genes in a collection of Setaria genotypes from North America and Eurasia, and identify the occurrence of novel and known target-site mutations that led to resistance. A total of 214 Setaria genotypes were exposed to commonly used herbicides that inhibit specific genes: herbicide action class (HRAC) group 1 herbicides targeting acetyl-CoA carboxylase (ACCase), HRAC 2 targeting acetolactate synthase (ALS), HRAC 9 targeting 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase, and HRAC 10 targeting glutamine synthetase. ACCase and ALS genes in 53 accessions were PCR-amplified and sequenced. Whole-genome sequencing reads covering the target genes were analyzed for an additional 98 genotypes. Herbicide trials showed that 30% of our accessions set seed following application of at least one herbicide, and 13 accessions were resistant to multiple classes of herbicides. Although there were numerous SNPs, including some known to lead to resistance, in our target genes, SNPs found predominantly in herbicide-resistant genotypes were largely intronic or synonymous. A small number of amino acid substitutions in ALS and ACCase indicated potential and incomplete resistance to HRAC 1 and 2 herbicides, but no SNPs putatively associated with herbicide resistance were identified in the other 6 target-site genes. The broader pattern of herbicide resistance in S. viridis is likely driven by non-target mutations that detoxify or compartmentalize applied herbicides.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"139 6","pages":""},"PeriodicalIF":4.2,"publicationDate":"2026-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13144258/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147843227","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":"First brassinosteroid-based dwarf mutant discovered and characterized in grapevine.","authors":"Yingzhen Yang, Jie Arro, Cheng Zou, Madeline Oravec, Bruce Reisch, Gan-Yuan Zhong","doi":"10.1007/s00122-026-05225-6","DOIUrl":"10.1007/s00122-026-05225-6","url":null,"abstract":"<p><p>In this study, we investigated the genetic control of dwarfism in naturally occurring dwarf mutant lines of grapevines. Through trait-segregation and marker-trait association analyses, we identified a major locus on Chromosome 14 tightly associated with the dwarf trait. Subsequently, we conducted a bulked RNA-seq analysis, fine mapped the dwarf trait and identified VviBR6OX1, a cytochrome P450 enzyme involved in brassinosteroid synthesis, as a candidate gene for the observed dwarfism. RNA-seq sequence analyses revealed two in-frame deletions in the gene: a 12-bp deletion in exon 1 and a 9-bp deletion in exon 4. A survey of the two indels in Vitis germplasm suggested that the 9-bp deletion is most likely the cause of dwarfism in the mutant. We recreated similar dwarf grapevines by knocking out VviBR6OX1 using CRISPR/Cas9 gene editing and confirmed VviBR6OX1's role in controlling vine architecture. Additionally, we observed several vines with an extreme compact dwarf phenotype and determined that the compact dwarfing phenotype was a result of simultaneous editing of a second BR6OX gene, VviBR6OX2. The discovery of BR-related dwarfism in grapevine provides an important genetic avenue for developing desirable vine architecture for various breeding purposes.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"139 5","pages":""},"PeriodicalIF":4.2,"publicationDate":"2026-05-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13139300/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147821169","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":"Mutation of BrDAD1 affects flower opening and anther dehiscence by regulating jasmonate-mediated BrMYB108-BrSWEET15 module.","authors":"Tianer Tang, Zifan Zhao, Shunuo Li, Shanshan Ren, Qingli Hou, Luyao Zhang, Chong Tan, Yun Zhang, Xueling Ye, Zhiyong Liu","doi":"10.1007/s00122-026-05248-z","DOIUrl":"https://doi.org/10.1007/s00122-026-05248-z","url":null,"abstract":"<p><strong>Key message: </strong>BrDAD1 encodes a phospholipase A1 family protein and was precisely localized using MutMap technology. Allelic mutations and functional complementation experiments using Arabidopsis T-DNA insertion mutants demonstrated that BrDAD1 regulates petal opening and anther dehiscence by controlling jasmonic acid synthesis in Chinese cabbage. Flower opening and anther dehiscence are crucial for the successful reproduction of cross-pollinated crops. The role of jasmonic acid (JA) in floral organ development and fertility regulation has been extensively documented. However, its function in Chinese cabbage (Brassica rapa L. ssp. pekinensis) remains poorly characterized. In this study, three mutant plants, M5068, M5036 and M5088, with defects in flower opening and anther dehiscence were screened from a Chinese cabbage ethyl methane sulfonate-induced mutation library. Through genetic analysis, allelic tests, and MutMap, we identified that these three mutants each harbored non-synonymous mutations at distinct sites within the BrDAD1 gene, which encodes a phospholipase A1 family protein critical for JA biosynthesis. The mutation led to a significant reduction in JA in the M5068 mutant. Notably, exogenous application of methyl jasmonate can completely restore the phenotype of M5068. In addition, overexpression of BrMYB108 rescued the delayed flower opening and impaired anther dehiscence phenotypes in dad1, which results from JA deficiency in Arabidopsis thaliana. Further evidence from yeast one-hybrid, dual-luciferase reporter, and electrophoretic mobility shift assays revealed that BrMYB108 regulates flower opening and anther dehiscence by activating the promoter activity of BrSWEET15. This study identifies a novel regulatory mechanism of JA in flower opening and anther dehiscence, providing new insights into molecular mechanisms underlying floral organ development in Chinese cabbage. It also offers new targets and strategies for the application of male sterile lines in hybrid breeding.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"139 5","pages":""},"PeriodicalIF":4.2,"publicationDate":"2026-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147821164","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 of the TdHLS gene controlling hairy leaf sheath from wild emmer wheat.","authors":"Nannan Liu, Wenxin Wei, Junna Sun, Zuhuan Yang, Wei Pan, Xiaoming Xie, Jiazheng Yu, Jiarui Zhang, Boyuan Zhang, Weilong Guo, Yinghui Li, Qixin Sun, Jun Ma, Chaojie Xie","doi":"10.1007/s00122-026-05231-8","DOIUrl":"https://doi.org/10.1007/s00122-026-05231-8","url":null,"abstract":"<p><strong>Key message: </strong>The TdHLS gene controlling hairy leaf sheath derived from wild emmer wheat was fine-mapped to a ~2.3 Mb physical interval on chromosome 4BL based on the Zavitan (WEW_v1.0) reference genome. Trichomes on leaf sheaths serve as specialized epidermal structures that form a protective barrier for plants. Wild emmer wheat (WEW), a tetraploid progenitor of common wheat, represents a valuable genetic resource for wheat breeding programs. This study reported the fine mapping of TdHLS, a gene controlling hairy leaf sheath that was introgressed from WEW. Genetic mapping by F₂ and F₃ (0T267/Han 87-1*2 and 0T267/AK58*2) individuals revealed this gene was delimited in a 2.3 Mb region on chromosome 4BL based on the WEW reference genome (Zavitan v1.0), and this region shows observed recombination suppression. Transcriptomic and sequence analyses identified four expressed genes containing nonsynonymous mutations between hairy and glabrous leaf sheath lines, within the 28 annotated genes located in the target interval. Among them TRIDC4BG062310 (encoding an oxysterol-binding protein-related protein) exhibited differential expression patterns, suggesting its potential role in trichome development. Collinearity analysis indicated orthologous hairy leaf sheath loci in WEW (Zavitan v1.0), barley (Morex v1.0) and Aegilops tauschii (AL8/78 v4.0), indicating the presence of evolutionarily conserved homologous genes governing this morphological characteristic. Introgression lines demonstrated successful trait incorporation without affecting plant architecture and grain characteristics. This study establishes a foundation for cloning the TdHLS gene and provides a valuable morphological marker for wheat breeding.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"139 5","pages":""},"PeriodicalIF":4.2,"publicationDate":"2026-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147821196","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 candidate genes for deep-sowing tolerance in rice by genome-wide association study and transcriptome sequencing.","authors":"Chenghang Tang, Guohui Dou, Di Bai, Wenhao Lv, Chunni Wang, You Zhou, Meng Zhang, Xingmeng Wang, Yaling Bao, Arabboevich Ergashev Mukhammadjon, Manqiong Zhu, Yingyao Shi","doi":"10.1007/s00122-026-05235-4","DOIUrl":"https://doi.org/10.1007/s00122-026-05235-4","url":null,"abstract":"<p><p>Direct-seeded rice is of great significance for ensuring food security. The hypoxic conditions under deep sowing impose significant abiotic stress to severely inhibit seed germination and seedling emergence in direct-seeded rice. Improvement of rice tolerance to deep-sowing germination stress is critical for promoting the seedling and grain yield of direct-seeded rice. In this study, we employed 276 rice germplasms to investigate the hypoxic germination (HG)-related traits through genome-wide association study (GWAS). Transcriptome profiling was conducted on germplasms with strong and weak HG tolerance under both deep-sowing and control conditions. GWAS identified 76 HG-associated genes, among which 27 genes were also detected by transcriptome profiling. Gene functional annotation and haplotype analysis screened four important candidate genes (LOC_Os01g51870, LOC_Os03g11510, LOC_Os05g01440, and LOC_Os07g35350) related to HG under deep sowing. The findings establish a genetic framework for improving HG tolerance in rice under deep sowing through molecular breeding strategies.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"139 5","pages":""},"PeriodicalIF":4.2,"publicationDate":"2026-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147781818","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 of soybean germplasm derived from modern Canadian and Chinese soybean cultivars to identify novel genes conferring soybean cyst nematode resistance.","authors":"Scott Moore, Owen Wally, Albert Tenuta, Mohsen Yoosefzadeh Najafabadi, Christopher Grainger, Milad Eskandari, Istvan Rajcan","doi":"10.1007/s00122-026-05243-4","DOIUrl":"https://doi.org/10.1007/s00122-026-05243-4","url":null,"abstract":"<p><strong>Key message: </strong>Developing genetically resistant soybean cultivars is key in controlling the most damaging soybean disease worldwide; soybean cyst nematode (SCN) is critical for soybean production. Development and spread of new HG types of SCN that break down current resistance genes warrant continuous efforts to identify novel resistance sources. Here, a GWAS study in a diversity panel consisting of modern Canadian and Chinese soybean cultivars was used to identify novel marker-trait associations in the soybean genome derived from Chinese germplasm. Soybean cyst nematode (SCN), caused by Heterodera glycines Ichinohe, is the most destructive pathogen affecting soybean production in North America. Overreliance on plant introduction (PI) 88788 as a resistance source in commercial soybean cultivars has led to SCN field populations shifting toward virulence against this resistance source. Modern Chinese soybean cultivars have emerged as potential sources of both known and novel SCN resistance genes. This study aimed to investigate the genetics underlying HG-type 2.5.7 SCN resistance in a genomic diversity panel (n = 201) comprised of modern Canadian (CD), Chinese (CH), and combined CD-CH soybean genotypes through a genome-wide association study (GWAS). Genotyping-by-sequencing (GBS) detected 15,932 single nucleotide polymorphisms (SNPs). Phenotypic SCN resistance was assessed by infesting genotypes in the GWAS panel using a greenhouse bioassay with HG-type 2.5.7 to calculate the female index (FI). FarmCPU detected one SNP on chromosome 9, explaining 7.26% of phenotypic variation in SCN resistance, while BLINK identified the same chromosome 9 SNP at 35.15% and two additional ones on chromosomes 8 and 13, explaining 24.81 and 15.92% variation, respectively. Alternative alleles for these SNPs were contributed by CH and CD-CH genotypes. Three candidate genes were identified in this study, in which Glyma.09g238800 appears to be the strongest, but verification is warranted in future research. The significant SNPs identified in this study show the genetic utility of modern Chinese soybean germplasm in developing soybean cultivars with alternative SCN resistance genes to enhance the sustainability of developing SCN-resistant soybean cultivars in North America.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"139 5","pages":""},"PeriodicalIF":4.2,"publicationDate":"2026-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147781821","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":"Characterization of stable grain protein content loci on chromosome 6D without adverse effect on yield traits in bread wheat.","authors":"Hang Liu, Chao Wang, Jiating Chen, Huaping Tang, Tongzhu Wang, Md Nahibuzzaman Lohani, Hafiz Muhammad Faisal Umer, Muhammad Junaid Jalil, Haopeng Zhang, Xia Yang, Qiang Xu, Jian Ma, Guangdeng Chen, Meijin Ye","doi":"10.1007/s00122-026-05253-2","DOIUrl":"https://doi.org/10.1007/s00122-026-05253-2","url":null,"abstract":"<p><strong>Key message: </strong>This study identified and validated novel QTL controlling GPC, predicted the underlying candidate genes, and provides valuable insights for improving wheat nutritional quality while minimizing yield penalties. Grain protein content (GPC) is a key determinant of wheat quality, but its improvement is often limited by a negative correlation with yield. To elucidate the genetic architecture of GPC, a genome-wide association study was conducted on 224 wheat cultivars genotyped with a 120 K SNP array and phenotyped across three environments. We identified three stable quantitative trait loci (QTL) on chromosome 6D, QGPC.sau-SCV-6D.1, QGPC.sau-SCV-6D.2, and QGPC.sau-SCV-6D.3 which were consistently detected across environments and in best linear unbiased prediction analyses. These loci explained 4.94-9.12% of the phenotypic variance. Notably, the GPC increasing alleles exhibited no adverse effect on major yield components, including thousand-grain weight and grain number per spike. Validation in two independent recombinant inbred line populations confirmed the stable effects of these three QTL. Candidate gene analysis within the QTL intervals highlighted five genes with putative roles in regulating GPC. These findings establish chromosome 6D as a valuable genomic region for breeding high-protein wheat and provide practical markers for marker-assisted selection with minimal yield penalties.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"139 5","pages":""},"PeriodicalIF":4.2,"publicationDate":"2026-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147781852","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 combination of QTL mapping and genome‑wide association study revealed key genes for heat tolerance in maize.","authors":"Xining Jin, Hangdan Qu, Pingxi Wang, Huaisheng Zhang, Tiantian Li, Xiangyuan Wu, Shilin Chen, Yaqiu Zhao, Fei Wang, Rui Song, Zhiyuan Fu, Xiaoxiang Zhang","doi":"10.1007/s00122-026-05206-9","DOIUrl":"https://doi.org/10.1007/s00122-026-05206-9","url":null,"abstract":"<p><strong>Key message: </strong>Integrated QTL GWAS identified three key genes, whose heat ind uction during maize germination was verified via RNA seq and qRT PCR analysis. Heat stress during germination critically impairs maize seedling establishment and yield stability, yet its genetic basis remains poorly understood. Here, 21 quantitative trait loci (QTLs) for heat tolerance were identified in a recombinant inbred line (RIL) population under heat stress (39 °C vs. 28 °C), including a major hypocotyl diameter QTL (qHDT2-1, LOD = 23.68). Concurrently, genome-wide association study (GWAS) in an association panel detected 213 significant SNPs associated with heat tolerance. Population-stable SNPs, pleiotropic SNPs and high-impact QTLs were integrated to identify candidate genes. Transcriptome analysis and GO enrichment prioritized 612 candidate genes, among which six heat-induced genes were selected. Subsequent validation confirmed Zm00001d005300, Zm00001d023524, and Zm00001d026563 as core regulators forming a coordinated heat-response network. We also found that heat stress had a relatively minor impact on germination rates, but significantly affects biomass accumulation and tissue morphology. This study identifies key genetic targets for breeding heat tolerant maize.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"139 5","pages":""},"PeriodicalIF":4.2,"publicationDate":"2026-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147781784","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}