Theoretical and Applied Genetics最新文献

{"title":"Map-based cloning of Zmccr3 and its network construction and validation for regulating maize seed germination.","authors":"Liqing Feng, Mingting Zhou, Anyan Tao, Xiaolin Ma, Nan Wang, He Zhang, Huijun Duan, Yongsheng Tao","doi":"10.1007/s00122-025-04890-3","DOIUrl":"https://doi.org/10.1007/s00122-025-04890-3","url":null,"abstract":"<p><strong>Key message: </strong>Map-based cloning of Zmccr3 for regulate SG and its molecular regulatory pathway was performed and validated. WGCNA, target genes/pathways during the process of seed dormancy formation were obtained. Seed dormancy (SD) and pre-harvest sprouting (PHS) affect the grain yield and quality of grain in cereal and hybrid seed production. Although the benefits of studying SD and seed germination (SG) during seed development are well established, research into the genetic variation and molecular regulation of SD, particularly during the transition from SD to SG, remains very limited. In this study, bulked segregant analysis (BSA) and linkage analysis were used to map the QTL for the maize vp16 mutant of PHS. Using genetic and biological methods, the candidate gene was identified as Zmccr3, encoding cinnamoyl-CoA reductase 3 (ccr3), which is involved in the phenylalanine pathway of lignin metabolism and affects SG. Based on RNA-seq (RNA sequencing) at two stages of grain development with extreme PHS traits, a weighted gene coexpression network analysis (WGCNA) related to SD and SG formation was constructed, and ten target genes and three pathways during the transition from SD to SG were identified. Simultaneously, the Zmccr3 pathway was established and validated, involving upstream lipid metabolism, redox modification and degradation of cell wall oligosaccharides (as electrophilic compounds), regulation of GA signaling and intracellular ROS homeostasis, and downstream oxidation of cell wall lignin units and synthesis of phenolic compounds that affect endosperm weakening and cell wall loosening, ultimately regulating SG or SD. Therefore, we propose the Zmccr3 hypothesis to elucidate its possible functions. These findings have important theoretical and practical implications for understanding the genetic basis of PHS and SD in maize, increasing genetic resources and improving traits.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 5","pages":"105"},"PeriodicalIF":4.4,"publicationDate":"2025-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144014764","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":"OsBSK3 and OsBSK2 regulate grain size and leaf angle via MAPK signaling pathway in rice.","authors":"Xin Jin, Linli Fu, Chunxiao Chen, Jiali Liu, Yingxiang Liu, Wei Zhang, Xiufeng Li, Changhua Liu, Qingyun Bu, Xiaojie Tian","doi":"10.1007/s00122-025-04889-w","DOIUrl":"https://doi.org/10.1007/s00122-025-04889-w","url":null,"abstract":"<p><p>Grain size and leaf angle are key agronomic traits that determine the final yield. OsBSKs (BRASSINOSTEROID-SIGNALING KINASES) and OsMAPKs (MITOGEN ACTIVATED PROTEIN KINASE) are known to play essential roles in plant growth, development, and stress responses. However, the potential crosstalk between these pathways and their specific roles in regulating grain size and leaf angle remain largely unexplored in rice. Here, we characterized that OsBSKs regulate grain size and leaf angle in rice, and among these, OsBSK2 and OsBSK3 may play more critical roles. The grain size and leaf angle in osbsk3 and osbsk2 mutants are significantly smaller, whereas the OsBSK3-overexpressing lines (OsBSK3-OEs) exhibit considerably larger grain size and leaf angle compared to the others. Furthermore, both OsBSK3 and OsBSK2 interact with OsMKKK10, indirectly activating OsMAPK6 in plant cells. Notably, mutations in MAPK cascade components, such as smg2-1 (an osmkkk10 mutant), smg1-1 (an osmkk4 mutant), and dsg1 (an osmapk6 mutant), resulted in significantly reduced leaf angles. Moreover, these mutations were able to rescue the increased grain size and leaf angle observed in OsBSK3 overexpression lines. Additionally, we also identified OsWRKY53 as a potential downstream target of the OsBSKs-OsMKKK10-OsMKK4-OsMAPK6 cascade in the regulation of grain size and leaf angle. Taken together, the above results not only highlight the essential and specific roles of OsBSK3 and OsBSK2 in regulating rice grain size and leaf angle, but also reveal the mechanism which OsBSK3/OsBSK2 mediate MAPK cascade to regulate rice grain size and leaf angle.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 5","pages":"104"},"PeriodicalIF":4.4,"publicationDate":"2025-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144054393","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":"EBMGP: a deep learning model for genomic prediction based on Elastic Net feature selection and bidirectional encoder representations from transformer's embedding and multi-head attention pooling.","authors":"Lu Ji, Wei Hou, Heng Zhou, Liwen Xiong, Chunhai Liu, Zheming Yuan, Lanzhi Li","doi":"10.1007/s00122-025-04894-z","DOIUrl":"https://doi.org/10.1007/s00122-025-04894-z","url":null,"abstract":"<p><p>Enhancing early selection through genomic estimated breeding values is pivotal for reducing generation intervals and accelerating breeding programs. Recently, deep learning (DL) approaches have gained prominence in genomic prediction (GP). Here, we introduce a novel DL framework for GP based on Elastic Net feature selection and bidirectional encoder representations from transformer's embedding and multi-head attention pooling (EBMGP). EBMGP applies Elastic Net for the selection of features, thereby diminishing the computational burden and bolstering the predictive accuracy. In EBMGP, SNPs are treated as \"words,\" and groups of adjacent SNPs with similar LD levels are considered \"sentences.\" By applying bidirectional encoder representations from transformers embeddings, this method models SNPs in a manner analogous to human language, capturing complex genetic interactions at both the \"word\" and \"sentence\" scales. This flexible representation seamlessly integrates into any DL network and demonstrates a marked improvement in predictive performance for EBMGP and SoyDNGP compared to the widely used one-hot representation. We propose multi-head attention pooling, which can adaptively assign weights to features while learning features from multiple subspaces through multi-heads for a high level of semantic understanding. In a comprehensive comparative analysis across four diverse plant and animal datasets, EBMGP outperformed competing models in 13 out of 16 tasks, achieving accuracy gains ranging from 0.74 to 9.55% over the second-best model. These results underscore EBMGP's robustness in genomic prediction and highlight its potential for deep learning applications in life sciences.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 5","pages":"103"},"PeriodicalIF":4.4,"publicationDate":"2025-04-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12009238/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144038938","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":"Association mapping of haploid male fertility in sweet corn.","authors":"Tyler L Foster, Ursula K Frei, Mercy Fakude, Matheus D Krause, Sarah Pfeffer, Somak Dutta, William F Tracy, Marcio F R Resende, Thomas Lübberstedt","doi":"10.1007/s00122-025-04888-x","DOIUrl":"https://doi.org/10.1007/s00122-025-04888-x","url":null,"abstract":"<p><strong>Key message: </strong>Association mapping of a subset of the SweetCAP diversity panel revealed ten single-nucleotide polymorphisms (SNPs) associated with haploid male fertility (HMF), which provided four candidate genes. Doubled haploid (DH) technology using in vivo haploid induction has dramatically improved the efficiency of maize breeding programs worldwide. However, limitations from genome doubling create a bottleneck for DH line production. To overcome such limitations, spontaneous haploid genome doubling (SHGD) has gained prominence over the last decade, specifically in field corn materials. On the contrary, SHGD in sweet corn has been largely overlooked. A subset of 286 sweet corn genotypes from the SweetCAP diversity panel was evaluated for their ability to restore male fertility in the haploid state, otherwise known as haploid male fertility (HMF). Association mapping identified ten single-nucleotide polymorphisms (SNPs) associated with HMF, which provided four candidate genes. Our results highlight significant variation for HMF, with 11 genotypes having > 54% HMF. These genotypes demonstrate HMF naturally exists in sweet corn germplasm and can be used for population improvement.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 5","pages":"102"},"PeriodicalIF":4.4,"publicationDate":"2025-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144049481","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":"Chromosomal structural variation loci HSS1 and HSS6 lead to hybrid sterility in rice.","authors":"Siqi Cheng, Zhenwei Xie, Hao Yu, Chaolong Wang, Xiaowen Yu, Jian Wang, Hai Zheng, Jiayu Lu, Xiaodong He, Keyi Chen, Junwen Gao, Yang Hu, Bowen Yao, Dekun Lei, Shimin You, Qiming Wang, Anqi Jian, Ling Jiang, Yulong Ren, Xiuping Guo, Yunlu Tian, Shijia Liu, Xi Liu, Shanshan Zhu, Zhigang Zhao, Jianmin Wan","doi":"10.1007/s00122-025-04887-y","DOIUrl":"https://doi.org/10.1007/s00122-025-04887-y","url":null,"abstract":"<p><strong>Key message: </strong>Chromosomal structural variation leads to rice hybrid sterility, and this study has established a new inheritance model and offers a novel insight into hybrid sterility in rice. The utilization of heterosis among different species significantly enhances rice yield. However, the direct application of this advantage is hindered by hybrid sterility (HS). Here we identify a stable semi-sterile inbred line (SSIL) in the hybridization between rice species O. sativa indica and wild rice O. longistaminata. Both pollen and spikelet fertility in heterozygous SSIL plants are semi-sterile, and the homozygous plants show normal fertility. Interestingly, unlike previously reported hybrid sterility loci, SSIL does not induce segregation distortion in progeny. The genotypes of chromosome 1 (Chr.1) exhibit tight pseudo-linkage on Chr.6 in SSIL population. HSS1 and HSS6 are named as the two loci of Chr.1 and Chr.6. Cytological observations revealed abnormalities in male and female gametes during meiosis, ultimately resulting in semi-sterile pollen and spikelet. HSS1 was narrowed down to a 190.6-kb interval and HSS6 to a 1391.6-kb region using an SSIL population of 10,393 plants. Through high-throughput sequencing and observation of chromosomal behavior during meiosis, a reciprocal translocation between the short arm of Chr.1 and the end of Chr.6 in the translocated RD23-type (R^T-type) gamete in SSIL was discovered. The presence of R^T-type gametes in SSIL is the direct causative factor for semi-sterility in both male and female gametes. This translocation led to abnormal SSIL-R^T/L synapses and the formation of tetravalent ring structures in chromosomes during pachynema. Our findings have uncovered a pair of reciprocal chromosome translocations that control reproductive isolation in rice. These insights offer valuable guidance for optimizing hybrid breeding applications, ultimately enhancing the benefits of heterosis.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 5","pages":"101"},"PeriodicalIF":4.4,"publicationDate":"2025-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144035876","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":"Temporal transcriptome analysis reveals the two-phase action of florigens in rice flowering.","authors":"Renwei Sun, Yifeng Ding, Manaki Mimura, Noriko Nishide, Takeshi Izawa","doi":"10.1007/s00122-025-04869-0","DOIUrl":"https://doi.org/10.1007/s00122-025-04869-0","url":null,"abstract":"<p><p>Two florigen genes, Hd3a and RFT1, are essential for the floral transition in rice. To elucidate the early steps of the transcriptional dynamics during rice floral induction, we compared a set of temporal transcriptome data of SAM (shoot apical meristem)-region samples between the wild-type and a non-flowering line of the hd3a rft1 double mutant during a short-day (SD) treatment after growing under long-day conditions for 42 days, and identified 6,978 DEGs (differentially expressed genes). As expected, FUL-like MADS-box genes were induced just after 4 days SD treatment; meanwhile, SEP-type and AGL-type MADS-box genes were induced after 9 days of SD treatment. We here newly revealed that majority of rhythmic genes including major circadian clock genes were not affected by the florigen genes, implying normal circadian clock phasing at the SAM regions regardless of floral transitions. We found that around two thousands of genes were repressed by Hd3a and RFT1 genes at the SAM regions before the SD treatments and become derepressed and similar to WT expression levels in the double mutants according to the SD treatments. These clearly imply two distinct actions of florigen genes: one for repression of some developmental key genes during vegetative growth possibly by very low level of florigen expression and the other for floral induction by relatively high florigen expressions upon short-day inductions. This repression by low levels of florigens may serve as a maintenance system for vegetative growth before floral induction, which implies a novel role for florigen genes in rice.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 5","pages":"100"},"PeriodicalIF":4.4,"publicationDate":"2025-04-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11993458/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144035640","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 of identity by descent reveals genes shaping morphology and biological traits in the cultivated lettuce varieties during the long-term crossbreeding.","authors":"Qianqian Zhang, Bo Cui, Xinyu Dong, Wenjun Lv, Xueying Xie, Yujue Wang, Zhongxu Guo, Just Jensen","doi":"10.1007/s00122-025-04879-y","DOIUrl":"https://doi.org/10.1007/s00122-025-04879-y","url":null,"abstract":"<p><p>The domestication of lettuce (Lactuca sativa L.) has resulted in its unique leaf morphology, making it one of the most widely consumed vegetable crops worldwide. The development of sequencing technology provides the opportunity to thoroughly investigate how the genomic variants contribute to the distinct morphology and biological traits of various major cultivated lettuce varieties such as Butterhead, Crisphead and Cos, which remains largely unknown. First, we present the phylogeny of the cultivated lettuce varieties and population structure of the sequenced represented cultivated lettuce varieties. We then utilized the method of relative Identity by descent (rIBD) to map the genomic regions and genes that show evidence of shared ancestry and selection in the pair-wised comparisons of these varieties. The average rIBD scores of 0.063, 0.093 and 0.187 were observed between Butterhead and Cos, Butterhead and Crisphead, Crisphead and Cos, respectively, and we further employed the Fixation index and integrated haplotype score method to validate whether these genomic regions are also under selection. We have identified candidate significant genes such as WOX2, GT5, RZ1B, ATPK2 and HIRA which play key roles in seed development, anthocyanins 3-O-glucosyltransferase activity and the accumulation of anthocyanin pigment, tolerance to cold stress, plant disease resistance and tolerance to heavy metal cadmium and leaf development during long-term cross-breeding and selection. Our relative identity by descent mapping reveals critical functional genes under selection shaping morphology and biological traits in the cultivated lettuce varieties throughout long-term crossbreeding.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 5","pages":"99"},"PeriodicalIF":4.4,"publicationDate":"2025-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143987085","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 Golden2-like transcription factor regulates Brassica napus seed vigor after artificial aging.","authors":"Xiaoke Ping, Mei Yan, Jia Wang, Qianjun Ye, Taiyuan Zhang, Xiaojie Hu, Sheng Chen, Jiana Li, Liezhao Liu","doi":"10.1007/s00122-025-04884-1","DOIUrl":"https://doi.org/10.1007/s00122-025-04884-1","url":null,"abstract":"<p><strong>Key message: </strong>A novel GLK transcription factor, BnaA03.G2-like, regulates seed vigor after aging by affecting FAs composition in B. napus. Seeds, a most crucial materials for crop production, constitute the basis of agriculture. Seed aging usually occurs during storage, especially for seeds with high oil content. However, the genes and mechanisms underlying seed aging in Brassica napus, a widely grown oilseed crop, remain largely unexplored. In this study, nine SNPs associated with seed vigor after aging were identified through a genome-wide association study, and transgenic seeds confirmed that BnaA03.G2-like negatively regulated seed vigor after aging. Haplotype and gene-based association analyses revealed that S_A3.16900957 and S_A3.16901008 were two core variants located within BnaA03.G2-like. Transcriptome analysis and gas chromatography results suggested that BnaA03.G2-like regulated fatty acid biosynthesis, and the linoleic acid content significantly increased in the seeds of BnaA03.G2-like overexpression lines but decreased in the seeds of BnaA03.G2-like RNA interference lines. Further correlation analysis and malondialdehyde determination revealed that BnaA03.G2-like regulated seed vigor by affecting the linoleic acid content in mature seeds and the degree of membrane lipid peroxidation during seed aging. This study initially reported the function of BnaA03.G2-like and its favorable alleles, providing genetic resources for seed antiaging breeding in B. napus.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 5","pages":"98"},"PeriodicalIF":4.4,"publicationDate":"2025-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144043453","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 chromosome-scale genomes of two cultivated safflowers (Carthamus tinctorius) provide insights into the genetic diversity resulting from domestication.","authors":"Shuo Liu, Saimire Aishan, Qiuyu Liu, Lu Lv, Kang Ma, Kangjun Fan, Kehui Zhang, Yonghua Qin, Gang Li, Xueli Hu, Zunhong Hu, Junwei He, Hong Liu, Rui Qin","doi":"10.1007/s00122-025-04874-3","DOIUrl":"https://doi.org/10.1007/s00122-025-04874-3","url":null,"abstract":"<p><strong>Key message: </strong>Two cultivated safflowers from distinct areas elucidate the genetic diversity present in the linoleic acid biosynthesis, flowering time and flavonoid biosynthesis. The process of domestication facilitates the adaptation of crops to agricultural environments. In this study, we selected two representative safflower cultivars that has been domesticated in two distinct areas in China as samples to investigate their genetic diversity due to local environmental adaption. Yunhong-7 is a locally bred safflower (Carthamus tinctorius) cultivar, that has been currently widely cultivated in Yunnan Province, Southwest China, and Anhui-1 is a safflower cultivar that was locally bred in Anhui Province, East China. We firstly generated the chromosome-scale genome assembly for yunhong-7 cultivar by combining PacBio and Hi-C technologies. Through comparative genomic analysis, we identified structural variations (SVs) between yunhong-7 and anhui-1, which revealed their genetic differences in the pathways of fatty acid biosynthesis, circadian rhythm and flavonoid biosynthesis. Subsequently, a total of 40 non-redundant fatty acid desaturase 2 (FAD2) genes (39 for yunhong-7 and 20 for anhui-1) were identified, revealing the presence of copy-number variation and major genes change between yunhong-7 and anhui-1. The presented results suggested that changes in SVs may induce alterations in the expression of flowering-related genes, which could explain the observed early flowering phenotype in yunhong-7 compared to anhui-1. We identified a total of 197 non-redundant UDP-glucuronosyltransferases (UGT) genes. Based on prokaryotic expression system, we investigated the catalytic functions of two unique UGT genes (CtUGT.18 and CtUGT.191). The current study increases our knowledge of genetic diversity among crop cultivars resulting from distinct domestication processes and thus could contribute to the advancement of traits research and the safflower breeding.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 5","pages":"97"},"PeriodicalIF":4.4,"publicationDate":"2025-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144054442","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":"Stable pleotropic loci controlling the accumulation of multiple nutritional elements in wheat.","authors":"Reem Joukhadar, Richard M Trethowan, Rebecca Thistlethwaite, Matthew J Hayden, James Stangoulis, Suong Cu, Josquin Tibbits, Hans D Daetwyler","doi":"10.1007/s00122-025-04877-0","DOIUrl":"https://doi.org/10.1007/s00122-025-04877-0","url":null,"abstract":"<p><p>Understanding the genetic basis of nutrient accumulation in wheat is crucial for improving its nutritional content and addressing global food security challenges. Here, we identified stable pleiotropic loci controlling the accumulation of 13 nutritional elements in wheat across diverse environments using a large wheat population of 1470 individuals. Our analysis revealed significant variability in SNP-based heritability values across 13 essential elements. Genetic correlations among elements uncovered complex relations, with positive correlations observed within two distinct groups, where calcium (Ca), cobalt (Co), potassium (K), and sodium (Na) formed one group, and copper (Cu), iron (Fe), magnesium (Mg), manganese (Mn), molybdenum (Mo), nickel (Ni), phosphorus (P), and zinc (Zn) formed the other. Negative correlations were observed among elements across both groups. Through MetaGWAS analysis, we identified stable QTL associated with individual elements and elements with high positive correlations. We identified 67 stable QTL across environments that are independent from grain yield, of which 56 were detected using the MetaGWAS analysis indicating their pleiotropic effect on multiple elements. A major QTL on chromosome 7D that can shift the phenotype up to one standard deviation compared to the mean phenotype in the population exhibited differential effects on multiple elements belonging to both groups. Our findings offer novel insights into the genetic architecture of nutrient accumulation in wheat and have practical implications for breeding programmes aimed at enhancing multiple nutrients simultaneously. By targeting stable QTL, breeders can develop wheat varieties with improved nutritional profiles, contributing to global food security and human health.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 5","pages":"95"},"PeriodicalIF":4.4,"publicationDate":"2025-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11982167/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144015447","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}