Theoretical and Applied Genetics最新文献

{"title":"Common genetic control for grain filling duration and kernel weight in grain sorghum.","authors":"Daniel Otwani, Colleen Hunt, Alan Cruickshank, Yongfu Tao, Anna M G Koltunow, David Jordan, Emma Mace","doi":"10.1007/s00122-026-05409-0","DOIUrl":"10.1007/s00122-026-05409-0","url":null,"abstract":"<p><strong>Key message: </strong>The genetic control of GFD in sorghum closely overlaps with that of grain size, is influenced by both pre- and post-anthesis processes, offering new opportunities for yield improvement through targeted breeding and inter-racial trait introgression. The duration of the grain filling period has been associated with yield increases in cereals including maize and sorghum. The genetic control of grain filling duration (GFD) is however not known in sorghum. This study explored the genetic variation and extent of genetic control for GFD in a diverse panel of sorghum genotypes (n=904), in three environments across two years. A genome wide association analysis revealed 86 QTLs, 46 of which collocated with 54 previously reported grain size candidate genes in sorghum, indicating a significant enrichment. Single marker analysis revealed that genomic regions associated with GFD were similarly associated with grain size. Interestingly, in silico expression analysis of candidate genes associated with GFD revealed that GFD could be associated with processes that happen both before and after anthesis contrary to the understanding that GFD was primarily associated with processes that happen post anthesis. Haplotype analysis of SbGS3 resolved 8 haplotypes associated with grain filling duration, 2 of which were exclusive to the Guinea and Asian durra racial groups revealing opportunities for trait introgression across sorghum racial groups. These results indicate considerable opportunity to increase grain yield in sorghum, by selecting for longer GFD and diverse inter racial crosses to improve the genetic diversity for GFD in sorghum. Sorghum breeders will find application of these results in diversifying trait selection to optimise yields in changing environments.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"139 11","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-10-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13658289/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149169061","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":"Targeted anthocyanin biofortification in black rice: a review of spatial metabolic control, growth-defence trade-offs and genotype-environment-management design.","authors":"Meilin Chen, Qiao Wei, Ke Liu, Shijie Shi, Liying Huang, Zhaoqiang Jin, Yunbo Zhang, Matthew Tom Harrison","doi":"10.1007/s00122-026-05401-8","DOIUrl":"10.1007/s00122-026-05401-8","url":null,"abstract":"<p><p>Black rice is a nutrient-dense whole grain in which anthocyanins accumulate predominantly in the outer caryopsis layers, but stronger pigmentation may impose carbon, energy and precursor demands that compromise yield, stress resilience and grain quality. This review synthesizes molecular and physiological controls of rice anthocyanin accumulation. It systematically evaluates whether relationships among anthocyanin content, grain yield, and eating, processing and nutritional quality are synergistic, antagonistic or unresolved. We present a targeted rather than constitutive biofortification framework integrating rice evidence on phenylpropanoid-flavonoid metabolism and the MYB-basic helix-loop-helix-WD40 transcriptional complex with candidate mechanisms involving epigenetic and post-transcriptional control, vacuolar transport and environmental signalling. Rice studies establish the roles of core pigmentation genes and document variation in grain anthocyanin composition. However, quantitative contributions of auxiliary regulators, transport pathways and environmental signalling remain incompletely validated in black-rice caryopses. We distinguish direct rice-grain evidence from other rice-tissue evidence and from cross-species or source-sink hypotheses. Both require grain-specific causal and field validation. We distinguish two breeding scenarios. One improves existing black-rice cultivars with endogenous, spatially organized pigmentation pathways. The other reconstructs grain-specific anthocyanin production in elite white-rice backgrounds and may require coordinated pathway completion and tighter control of tissue specificity and metabolic burden. We propose a Genotype × Environment × Management framework integrating spatial multi-omics, rice-specific validation, targeted editing, inducible regulation and precision agronomy. Restricting anthocyanin synthesis to appropriate tissues, developmental windows and carbon-replete conditions may improve nutritional value while maintaining yield stability, end-use quality and climate resilience.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"139 11","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-10-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149171195","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":"High-resolution GWAS and diagnostic functional marker development for leaf shape in soybean.","authors":"Le Wang, Yuan Zhang, Chun Li, Hongmei Qiu, Xiaoting Wen, Xinyue Wang, Jinshe Wang, Zhiqi Zhao, Xingjian Xu, Lichun Huang, Banghan Du, Hengyou Zhang","doi":"10.1007/s00122-026-05408-1","DOIUrl":"10.1007/s00122-026-05408-1","url":null,"abstract":"<p><strong>Key message: </strong>This study identified a major QTL governing leaf shape, pinpointed a highly associated SNP, and developed a dCAPSmarker, providing a useful molecular tool to facilitate marker-assisted breeding for leaf shape in soybean. Optimizing plant architecture to enhance canopy light distribution is a central objective in modern crop breeding. Leaf shape is a critical determinant of canopy structure and yield potential, yet the natural genetic variation underlying this trait in soybean remains underexploited for marker-assisted improvement. Here, we performed a genome-wide association study (GWAS) of leaf shape using a panel of 450 soybean accessions from northern China and identified a robust quantitative trait locus (qLS) for leaf shape on chromosome 20 that was consistently detected across multiple statistical models and two consecutive years. The lead SNP (SNP_35828042) resides within the second exon of GmJAG1 encoding a C2H2-type zinc finger transcription factor homologous to Arabidopsis JAGGED. This non-synonymous G/C variation results in an aspartic acid to histidine substitution (D9H) within the highly conserved EAR motif. Analysis of previously generated Cas9-edited GmJAG1 plants provided functional support for the role of GmJAG1 in regulating leaf shape. Population-level analysis revealed northward enrichment of the narrow-leaf-associated C allele, a pattern consistent with regional differentiation. We further developed a derived cleaved amplified polymorphic sequence (dCAPS) marker targeting the G/C polymorphism, which showed complete concordance with visual leaf-shape classification in the 41 tested accessions. This work provides population-scale validation of a GmJAG1-associated polymorphism, characterizes its geographical distribution, and delivers a practical molecular marker for screening soybean germplasm for leaf shape.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"139 11","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149115033","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":"Evaluating reaction norm and fixed effect models for genomic selection of end-use quality in wheat.","authors":"Jared Lile, Jennifer Lachowiec, Jason D Fiedler, Jason P Cook","doi":"10.1007/s00122-026-05394-4","DOIUrl":"10.1007/s00122-026-05394-4","url":null,"abstract":"<p><strong>Key message: </strong>Historic breeding program end-use quality data was used to perform genomic selection in two broad frameworks, incorporating fixed effect loci and genotype by environment interactions. Exceptional end-use quality in hexaploid bread wheat is an important factor for selling wheat in the global marketplace. However, many end-use quality traits are time-consuming and expensive to test, meaning their measurement is often delayed until late-stage trials of a breeding program. Genomic selection (GS) is one tool that has been shown to allow for earlier generation improvement of many traits in wheat breeding. Further, advances in GS methods may improve model predictive abilities, such as incorporating known loci that control traits as fixed effects and utilizing single-stage reaction norm models to control for genotype by environment interactions. Therefore, we evaluated conventional methods as well as these two advances to perform GS for twelve important end-use quality traits collected by the Montana State University (MSU) Spring Wheat Breeding Program from 2010-2022 across 842 elite breeding lines. We found that the conventional GS models performed well in 5-fold cross validation with predictive abilities ranging from 0.4-0.7 and in leave-one-year-out validation with most trait-year combinations exceeding a predictive ability threshold of 0.3. We did not observe any difference in predictive ability for the inclusion of fixed effect loci, but we did observe strong within-year correlations for the single-step reaction norm models in both validation methods. We concluded that both conventional, two-step GS and single-step reaction norm GS offer viable methods for earlier generation improvement of major end-use quality traits in the MSU Spring Wheat Breeding Program.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"139 10","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13638722/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149114754","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":"Candidate genes identification for internode length in rice via genome-wide association studies.","authors":"Bingxian Li, Jinghan Sun, Qiqi Yao, Yizhuo Ding, Yu Geng, Yaling Bao, Yang Ang, Hui Jiang, Zhen Yang, Yingyao Shi, Jianhua Jiang, Xiaojing Dang, Chaopu Zhang, Mukhammadjon Arabboevich Ergashev, Min Li, Jauhar Ali, Zhikang Li, Erbao Liu","doi":"10.1007/s00122-026-05395-3","DOIUrl":"10.1007/s00122-026-05395-3","url":null,"abstract":"<p><strong>Key message: </strong>Through GWAS and CRISPR/Cas9, it was found that INL1 and INL2 act as candidate genes regulating rice internodes and may affect the GA pathway. Their favorable haplotypes provide valuable gene targets for dwarf breeding. The number and length of each internode of rice are the determining factors of plant height, and are important traits for lodging resistance and yield formation. Mining the genes related to the number and length of internodes is of great significance for cultivating dwarf or semi-dwarf varieties. In order to explore the genetic basis of the number and length of internodes, the length and number of internodes in rice were determined for genome-wide association analysis, covering 429 accessions with 3.16 million high-quality single nucleotide polymorphisms. GWAS identified 34 significant marker-trait associations, found four new QTLs, and screened two candidate genes Internode number and length 1 (INL1) and INL2. They are annotated as cytochrome P450 enzymes and zinc finger protein transcription factors, respectively. These two family members are widely involved in plant physiological activities. The internode length and plant height of INL1 and INL2 knockout plants were lower than that of wild type. Transcriptomic analysis revealed that the loss of INL1 and INL2 suppresses differentially modulates gibberellin (GA) metabolism, ultimately leading to a dwarf phenotype. Haplotype analysis showed that the internode length of the HapA type of the two genes was lower than that of other haplotypes. Favorable alleles of OsINL1 and OsINL2 reduce height and can be further used in rice dwarf breeding to improve rice lodging resistance.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"139 10","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149115346","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":"BrANL2 negatively regulates the anthocyanin biosynthesis by depressing BrPAL, BrC4H, and Br4CL in purple flowering Chinese cabbage (Brassica rapa var. parachinensis).","authors":"Li Yuge, Xin Xiaoyun, Yu Shuancang, Li Peirong, Wang Weihong, Liu Yan, Zhao Xiuyun, Zhang Yaowei, Zhang Bin, Wang Jiao, Yu Yangjun, Zhang Fenglan, Su Tongbing, Zhang Deshuang","doi":"10.1007/s00122-026-05384-6","DOIUrl":"10.1007/s00122-026-05384-6","url":null,"abstract":"<p><strong>Key message: </strong>A new deep‑purple flowering Chinese cabbage germplasm (22M‑699) was developed, and BrANL2 was identified as a negative regulator of anthocyanin biosynthesis that directly represses BrPAL, BrC4H, and Br4CL, providing a target for purple-color breeding in Brassica crops. Purple flowering Chinese cabbage is highly valued in the market for its vibrant color and potential health benefits, especially the rich anthocyanin contents. Previously, we introduced the purple trait from mustard (Brassica juncea) into heading Chinese cabbage (Brassica rapa var. pekinensis) via distant hybridization, which resulted in a novel germplasm designated 18M-245. Subsequently, this purple trait was introgressed into flowering Chinese cabbage (Brassica rapa var. parachinensis) through hybridization and successive backcrossing, yielding another new germplasm named 22M-699, which exhibits uniformly deep-purple leaves similar to those of 18M-245. To investigate the genetic basis of the purple trait in purple flowering Chinese cabbage, we sequenced several genes involved in anthocyanin biosynthesis regulation. The results revealed insertions and large-fragment structural variations in the promoter region of BrANL2, which impair its transcriptional activity, leading to reduced expression in the purple germplasm 22M‑699. BrANL2 expression is negatively correlated with anthocyanin accumulation under low‑temperature conditions. Using DAP-seq and dual-luciferase reporter assays, we demonstrated that BrANL2 directly binds to the promoters of BrPAL, BrC4H, and Br4CL and represses their expression, thereby inhibiting anthocyanin biosynthesis. Furthermore, overexpression of BrANL2 reverses the purple phenotype in 22M-699, while its knockout induces purple pigmentation in a green line. Collectively, our findings reveal a suppressive role of BrANL2 targeting BrPAL, BrC4H, and Br4CL in anthocyanin biosynthesis in contrast to the previously reported positive functions of ANL2-like transcription factors and provide a potential strategy for generating purple materials in cruciferous vegetables.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"139 10","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149115390","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":"BSA-seq and fine linkage mapping for the identification of a novel locus (qNUE6) for nitrogen use efficiency in rice.","authors":"Yue Zou, Shupeng Xie, Yanze Zhao, Yuzhuo Liu, Wenzhong Zhang, Jiping Gao, Wei Xin","doi":"10.1007/s00122-026-05380-w","DOIUrl":"10.1007/s00122-026-05380-w","url":null,"abstract":"<p><p>Effective panicle number (EPN) is a major determinant of rice yield and is strongly influenced by nitrogen (N) availability. Identifying genes that maintain EPN under low-N conditions is therefore important for improving nitrogen use efficiency (NUE) in rice. In this study, bulked segregant analysis by sequencing (BSA-seq) of a recombinant inbred line (RIL) population comprising 1128 individuals identified a novel NUE-related quantitative trait locus, qNUE6. The locus was initially mapped to a 1.93 Mb interval on chromosome 6 and was subsequently narrowed to a 61.8 kb region through fine mapping of backcross-derived populations. Among the four annotated genes within the final interval, OsNRT1.2, which encodes a nitrate transporter, exhibited the strongest response to low-N treatment and was identified as the most likely candidate gene. Sequence comparison between the parental lines revealed one InDel and several SNPs, including promoter polymorphisms that may contribute to differential responses to low-N conditions. Functional analyses of overexpression and knockout lines demonstrated that OsNRT1.2 positively regulates nitrogen uptake, effective panicle number, grain yield, and overall NUE. Taken together, these results identify OsNRT1.2 as a strong candidate gene underlying qNUE6 and provide a useful molecular target for improving NUE in rice. However, broader validation across diverse germplasm and direct testing of the causal promoter variants is necessary to fully resolve the underlying mechanism.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"139 10","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149115385","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 studies reveal genomic regions for kernel-related traits in durum wheat.","authors":"Ana Laura Achilli, Pablo F Roncallo, Juan M Rodrigo, Curtis J Pozniak, Viviana C Echenique","doi":"10.1007/s00122-026-05379-3","DOIUrl":"10.1007/s00122-026-05379-3","url":null,"abstract":"<p><p>Kernel size and shape-related traits affect grain yield and semolina milling potential, both of which are important targets of durum wheat improvement programs. However, the genetic basis of these traits in durum wheat are largely unknown. In this study, we examined the genetic bases of kernel size and shape-related traits in a diverse panel of 170 genotypes, comprised mostly of Argentinian cultivars. Genotypes were characterized phenotypically in four field experiments in Argentina and genotypically using the 35K Axiom Wheat Breeder SNP Array. High phenotypic variability and heritability values were observed for all studied traits. Thousand kernel weight showed strong correlations with kernel area and factor form density, followed by kernel width, length and perimeter. Using genome-wide association mapping, a total of 80 marker-trait associations (MTAs) were identified over the FDR threshold (P < 0.00001). Of them, 23 MTAs were identified for best linear unbiased predictors (BLUPs) across the four environments or at least in two single environments, and ten SNPs located on 1B, 2A, 2B, 3B, 6A, and 7A chromosomes were identified by multiple mapping methods. Three of these SNPs, located on chromosome 2A, were selected as particularly interesting since they were identified by all three mapping methods tested. Two haplotype blocks (of 24.2 and 16.6 Mb) contain the SNPs of chromosome 2A, and both were strongly associated with most kernel traits. These haplotypes were not linked to Ppd-A1 gene and thus represent promising targets for further validation and implementation in molecular assisted breeding to improve kernel related traits in durum wheat.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"139 10","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149114719","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 effect of selection on allele frequencies and diversity in wheat (Triticum aestivum).","authors":"Mirai Inaoka, Carlos Ignacio, Nelly Arguello-Blanco, Lenin Rodrigues Betancourth, Clay Sneller","doi":"10.1007/s00122-026-05367-7","DOIUrl":"https://doi.org/10.1007/s00122-026-05367-7","url":null,"abstract":"<p><strong>Key message: </strong>Advancing wheat lines through stages of testing resulted in large genome changes. Consistent changes across cohorts and selection stages were noted though most changes appeared specific. Diversity was lost within a cohort, primarily at the last stage of advancement, though diversity across cohorts was not greatly impacted. The results can be used to develop informed crossing strategies. Effective selection increases the frequency of favorable alleles but can reduce genetic variation. The extent of allele frequency changes (AFC) that occur as wheat lines are advanced through stages of testing is not well documented. Our objectives were to determine the magnitude of AFC in a wheat breeding program, determine the consistency of AFC, and the effect of selection on population structure and diversity. We calculated the AFC for 1,173 markers on 4,678 wheat lines from ten cohorts that went through four stages of selection, primarily for yield. We determined the AFC for 48,093 marker/cohort/selection stage combinations and determined that 23.5% of these AFC's were greater than expected by drift and were attributed to selection. Most large AFC occurred in the final stage of selection. Eighty-nine markers had AFCs that showed signs of consistent unidirectional selection over cohorts and stages of selection, while 68.3% of the AFCs attributed to selection were cohort/selection-stage and directional specific. Within a cohort an average of 24.1% of makers had become fixed in stage-4 of testing, though few markers become fixed in more than one cohort. Each cohort experienced somewhat unique genome changes, likely due to selection in a unique array of environments. The genetic distance between cohorts of lines in stage-4 testing was similar to that among stage-1 lines. Crossing among the best lines from multiple cohorts would mitigate the loss of diversity within a single cohort and likely recombine favorable alleles selected across a wide array of environments.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"139 10","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13630794/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149114834","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":"Univariate and multivariate QTL analyses provide insights into genetic architecture of variation of key volatile aroma compounds in cucumber (Cucumis sativus L.).","authors":"Thi Nhien Hao Nguyen, Cassidy Duan, Uijeong An, Oyindamola Akinpelu, Yassine Yahia, Xiaofen Du, Yiqun Weng","doi":"10.1007/s00122-026-05393-5","DOIUrl":"https://doi.org/10.1007/s00122-026-05393-5","url":null,"abstract":"<p><strong>Key message: </strong>Univariate and multivariate (PC-based) QTL analyses in multiple segregating populations and environments identify 284 QTL and 52 PC-QTL for 24 volatile aroma compounds in cucumber, including two environmentally stable QTL clusters, each harboring 26 and 25 QTL for major C₆/C₉ alcohols and aldehydes, respectively. Consumers enjoy cucumber for its refreshing sensation, which is primarily associated with volatile organic compounds (VOCs) produced by the lipoxygenase biosynthesis pathway. However, our knowledge of cucumber flavor genetics remains limited. Here, we report QTL mapping of VOCs in multiple segregating populations grown under greenhouse and open-field conditions. VOC abundance exhibited highly quantitative inheritance with strong environmental effects and low broad-sense heritability. Transgressive segregation and underdominance were observed for most VOCs. Univariate QTL analysis identified 284 QTL for 24 VOCs, averaging 17 QTL for the six most abundant and aromatically significant VOCs. Both additive and dominance effects contributed significantly to VOC variation. Consistent with the strong correlation among many VOCs, 154 of the 284 QTL were co-localized into 15 distinct clusters. Multivariate principal component (PC)-based QTL analysis identified 52 PC-QTL that captured the maximum covariances among VOCs. Results from both methods were highly congruent, including the identification of two population-independent and environmentally stable QTL clusters, each harboring 26 and 25 QTL for major C₆/C₉ alcohols and aldehydes, respectively. The cos² and loading patterns of PCs mapped to these QTL clusters suggested closely linked loci rather than pleiotropic effects. Analysis of sequence variation and expression of annotated genes inside the two clusters identified several transcription factor genes as potential candidates. This study reveals a complex genetic architecture of VOC variation in cucumber. We discuss the results in the context of allele effects, segregation distortion, the association between QTL clustering and the LOX pathway, and implications for cucumber breeding for flavor enhancement.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"139 10","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13630885/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149115069","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}