Theoretical and Applied Genetics最新文献

{"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":"https://doi.org/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":"","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":"","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":"https://doi.org/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":"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":"https://doi.org/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":4.4,"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":"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":4.4,"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":"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":"https://doi.org/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":4.4,"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}

{"title":"Development and molecular cytogenetic characterization of black-grain wheat derived from wheat-Thinopyrum intermedium hybridization.","authors":"Chunfei Wu, Xinyu Zhao, Mingyao Li, Yunfeng Qu, Xinyu Yan, Jiarui Ding, Tong Zhou, Changtong Jiang, Qiaohan Liu, Jiarui Jiang, Xinling Li, Hongjie Li, Yanming Zhang","doi":"10.1007/s00122-025-04968-y","DOIUrl":"https://doi.org/10.1007/s00122-025-04968-y","url":null,"abstract":"<p><strong>Key message: </strong>Thirteen black-grain wheat lines with black endosperm and high grain protein were developed through hybridization between wheat cultivars and Thinopyrum intermedium. These lines are disomic chromosome substitution lines designated DS4B/4J^r/St or DS4D/4J^r/St. Thinopyrum intermedium (Host) Barkworth and D. R. Dewey (2n = 6x = 42, StStJ^rJ^rJ^vsJ^vs or StStEEEE) is a valuable genetic resource for wheat improvement. By crossing the common wheat cultivar Kehan 9 and a male-sterile line Taigu with Th. intermedium, we generated 13 wheat lines characterized by black aleurone and endosperm, along with elevated grain protein content. Field trials from 2022 to 2024 demonstrated that these lines exhibited superior yield traits and higher protein content compared to the parental Kehan 9. Sequential multicolor genomic and florescence in situ hybridization analyses revealed that a pair of recombinant J^r and St chromosomes from Th. intermedium replaced wheat chromosomes 4B or 4D, respectively. Single-nucleotide polymorphism (SNP) analysis via RNA-seq further identified this recombinant chromosome from the homoeologous group 4, designated 4J^r/St. These black-grain wheat lines were thus identified as disomic chromosome substitution lines DS4B/4J^r/St or DS4D/4J^r/St. Analysis of an F₂ population derived from a cross between black- and white-grain lines confirmed the association between chromosome 4J^r/St and the black-grain trait. Three anthocyanin-related genes located on chromosome 4J^r/St, and the expression level of Thint.S04G290300 encoding a basic helix-loop-helix (bHLH) DNA-binding superfamily protein, showed a progressive increase during grain development. Black pigmentation was initially detected at 18 days post-anthesis (DPA) in the aleurone layer near the embryo region and in the endosperm at 30 DPA. These lines provide a promising foundation for enhancing wheat nutritional value through the development of colored grain cultivars.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 8","pages":"184"},"PeriodicalIF":4.4,"publicationDate":"2025-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144660299","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":"Genetic variants of OsWRKY70 modulate ROS levels to improve rice stress adaptation.","authors":"Xiaoping Ding, GongYe Cheng, Di Zhang, Zhijun Wang, Mingchan Liu, Wenyu Li, Lingling Li, Ling Liu, Cheng Zheng, HouXiong Wu, Dingyang Yuan, Meijuan Duan, Citao Liu","doi":"10.1007/s00122-025-04953-5","DOIUrl":"https://doi.org/10.1007/s00122-025-04953-5","url":null,"abstract":"<p><strong>Key message: </strong>OsWRKY70 modulates ROS levels in rice to enhance tolerance to cold and salt stress. OsWRKY70^HapI reduces ROS and improves cold and salt tolerance, while OsWRKY70^HapII regulates ROS to increase salt tolerance and cold sensitivity, making OsWRKY70 a key target for improving rice stress resilience. Reactive oxygen species are essential in plant responses to abiotic stresses like drought, salinity, and extreme temperatures. In rice, the transcription factor OsWRKY70 plays a pivotal role in regulating ROS levels to enhance stress tolerance. This study examines two haplotypes of OsWRKY70, OsWRKY70^HapI and OsWRKY70^HapII, and their effects on rice resilience to cold and salt stress. Overexpression of OsWRKY70^HapI resulted in lower ROS accumulation, significantly improving cold tolerance by upregulating the antioxidant gene OsMYB4 and maintaining ion balance through OsMYB21 and OsAMTR1. In contrast, OsABA8ox1 led to higher ROS levels in OsWRKY70^HapII and increased sensitivity to cold stress, while still enhancing salt tolerance similar to OsWRKY70^HapI by regulating OsMYB21 and OsAMTR1. Haplotype analysis identified specific SNPs in OsWRKY70 that are critical for its transcriptional activity and stress response functions. Subcellular localization confirmed that OsWRKY70 operates as a nuclear transcription factor. These findings highlight the potential of OsWRKY70 haplotypes in genetic strategies to improve rice resilience to adverse environmental conditions by precisely modulating ROS and stress-responsive genes.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 8","pages":"183"},"PeriodicalIF":4.4,"publicationDate":"2025-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144620694","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":"Mutations of two AhTT8 genes reduce the accumulation of anthocyanins and confer the white testa of peanut (Arachis hypogaea L.).","authors":"Hailing Zi, Yaxin Ding, Ruiyuan Fang, Xinxin Li, Zhiyuan Song, Huailing Huang, Nana Li, Shoujin Fan, Chuanzhi Zhao, Xingjun Wang, Han Xia","doi":"10.1007/s00122-025-04966-0","DOIUrl":"https://doi.org/10.1007/s00122-025-04966-0","url":null,"abstract":"<p><p>Anthocyanins and proanthocyanidins (PAs), which determine the color of peanut seed coats, not only offer protection to plants under biotic and abiotic stress but also contribute to human health. The white testa peanut contains lower levels of anthocyanins and PAs, yet the mechanisms underlying the white testa phenotype in peanuts remain largely unknown. In the current study, two homologous peanut AhTT8 genes, namely AhTT8_AA and AhTT8_BB, were identified as the key genes controlling the seed coat color of peanuts through BSA-seq analysis and fine mapping. Null mutations or long sequence insertions were observed in two AhTT8 genes across six cultivated peanut varieties with white seed coat, and expression of AhTT8 genes was downregulated significantly in the white seed coat of peanuts. Overexpression of AhTT8 successfully restored PA and anthocyanin productions in Arabidopsis thaliana tt8 mutant. Furthermore, transcriptomic profiling of the seed coats of pink testa peanuts and white testa peanuts showed that expression of genes encoded transcription factors like AhMYB5, AhTTG1, AhMYB1, AhCPC, AhTTG2 and AhGL2 was downregulated in the white seed coats, while a subset of genes involved in PA and anthocyanin biosynthesis were also downregulated in the white seed coats. These results indicated that AhTT8 plays a central role in the regulation of peanut PA and anthocyanin biosynthesis, and resolving the molecular mechanisms of AhTT8 in peanuts is of great significance for peanut molecular breeding.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 8","pages":"182"},"PeriodicalIF":4.4,"publicationDate":"2025-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144609586","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":"Genomic analysis of two all-stage stripe rust resistance genes in the Vavilov wheat landrace AGG40807WHEA1.","authors":"Raghvendra Sharma, Chunhong Chen, Peng Zhang, Hemlata Bharti, Venu Kumaran Vikas, Michael Norman, Katherine Dibley, Adnan Riaz, Tim Hewitt, Sami Hoxha, Kerrie Forrest, Evans Lagudah, Harbans Bariana, Urmil Bansal, Lee Hickey, Sambasivam Periyannan","doi":"10.1007/s00122-025-04965-1","DOIUrl":"10.1007/s00122-025-04965-1","url":null,"abstract":"<p><strong>Key message: </strong>Comparative genomic analysis of two all-stage stripe rust resistance loci from Vavilov wheat landrace accession, AGG40807WHEA1, using Chinese Spring and 10 + hexaploid wheat genomes and validation of closely linked KASP markers. The ongoing occurrence and spread of wheat stripe rust, caused by the fungal pathogen Puccinia striiformis f. sp. tritici, threatens the global food security. Cultivation of varieties with effective sources of resistance is often followed by the appearance of virulent pathotypes at various times after their introduction. This requires an ongoing search for new sources. Tests of 296 accessions from the Vavilov wheat landrace collection identified numerous lines with broadly effective all-stage stripe rust resistance. Genetic analysis of one of these accessions (Australian Grains Genebank number AGG40807WHEA1) identified two all-stage resistance genes, temporarily named YrV1 and YrV2. The YRV1 and YRV2 loci were mapped to 3.48-3.98 and 730.2-731.2 Mb intervals in the short arm of chromosome 3B and the long arm of chromosome 7B, respectively. A comparative genomic analysis of the YRV1 locus in the Chinese Spring and the 10 + wheat pangenome databases revealed genomic rearrangements and lack of sequences encoding a nucleotide-binding and leucine-rich repeat (NLR) domain protein. Sequences belonging to NLR-like genes were present in the YRV2 region. Kompetitive allele-specific PCR (KASP) markers designed from SNPs IWB71814 and IWB69562, located at 0.4 cM and 0.5 cM distal to YrV1 and YrV2, respectively, were validated for marker-assisted selection using 123 hexaploid and 15 tetraploid wheat and 14 triticale cultivars. YrV1 and YrV2 genes are potentially valuable resources, and use of the closely linked molecular markers will expedite their deployment in breeding.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 8","pages":"180"},"PeriodicalIF":4.4,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12241163/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144601690","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":"Unraveling the genetic basis of maize ear diameter in a multi-parent RIL population derived from tropical and temperate germplasms.","authors":"Xiaoping Yang, Ranjan K Shaw, Fuyan Jiang, Guohong Wang, Xingming Fan","doi":"10.1007/s00122-025-04964-2","DOIUrl":"10.1007/s00122-025-04964-2","url":null,"abstract":"<p><strong>Key message: </strong>Based on WGS data, GWAS and QTL mapping jointly reveal the genetic mechanisms underlying maize ear diameter and identify candidate genes associated with this trait. Maize ear diameter is a crucial yield-related trait, yet its underlying genetic mechanisms remain largely undefined. To elucidate its genetic basis, a multi-parent population was developed from tropical and temperate maize germplasms. Employing a combined genome-wide association study and quantitative trait locus (QTL) mapping approach, five novel candidate genes (Zm00001eb032370, Zm00001eb050010, Zm00001eb303690, Zm00001eb023590, and Zm00001eb035700) and three key QTLs (qE1-1, qE1-5, and qE1-7) significantly associated with maize ear diameter were identified. Comprehensive analysis revealed that these candidate genes are involved in essential biological processes, including growth regulation, signal transduction, and stress responses, and likely modulate ear diameter through mechanisms such as hormone balance, cell division, and expansion. This study provides critical novel candidate genes for improving maize ear diameter and offers valuable insights into the molecular mechanisms regulating plant growth and development. Our findings not only enhance the understanding of maize developmental biology but also lay a theoretical foundation and offer new strategies for the genetic improvement of maize yield traits.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 8","pages":"181"},"PeriodicalIF":4.4,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12241290/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144601691","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}