Theoretical and Applied Genetics最新文献

{"title":"Identification and validation of a major QTL, QFhb-6AL, for Fusarium head blight resistance on chromosome 6AL in wheat.","authors":"Zhenzhen Zhu, Xuecheng Zhu, Na Zhang, Wenxi Wang, Jilu Liu, Fuping Zhang, Xiaomeng Ren, Yanpeng Ding, Fangyao Sun, Xi He, Sijia Hu, Xiuhua Li, Shurong Wei, Weilong Guo, Zhongfu Ni, Qixin Sun, Dongtao Liu, Zhenqi Su","doi":"10.1007/s00122-025-04864-5","DOIUrl":"https://doi.org/10.1007/s00122-025-04864-5","url":null,"abstract":"<p><strong>Key message: </strong>A novel major QTL, QFhb-6AL, accounting for 34.6% phenotypic variation for FHB resistance, was identified in the Chinese cultivar Xunong 029, and a near-diagnostic marker was developed for marker-assisted selection. Fusarium head blight (FHB) is a destructive disease in wheat (Triticum aestivum L.) that seriously threatens global wheat production and food safety. Host resistance is the most effective strategy for reducing FHB damage. The Chinese wheat cultivar Xunong 029 possesses desirable agronomic traits and demonstrates stable FHB resistance in multiple environments. A population of 190 F6 recombinant inbred lines (RILs) was developed by crossing Xunong 029 with Xumai 35 to identify quantitative trait loci (QTLs) for FHB resistance. The RIL population was genotyped by a low-coverage whole-genome sequencing (lcWGS) technology and evaluated for FHB symptom spread within a spike (Type II resistance) in both greenhouses and field experiments. A stable major QTL, designated as QFhb-6AL, was mapped to a 3.0 cM interval between markers lcWGS613.5 and lcWGS616.5 on the long arm of chromosome 6A, and it explained up to 34.6% of the phenotypic variation for FHB Type II resistance. QFhb-6AL was validated using near-isogenic lines (NILs) and another RIL population derived from the cross Xunong 029 and Xumai 33. Four kompetitive amplicon sequence PCR (KASP) markers which tightly linked to QFhb-6AL were developed. Haplotype analysis of the target QTL region showed a low frequency distribution of QFhb-6AL in Chinese cultivars, indicating that the QTL has not been widely deployed in wheat breeding programs. The QFhb-6AL has great potential for improving wheat FHB resistance, and the tightly linked markers developed in this study will facilitate its deployment in wheat breeding programs.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 4","pages":"74"},"PeriodicalIF":4.4,"publicationDate":"2025-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143634502","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":"Maize B chromosome affects the flowering time.","authors":"Paulo Maurício Ruas, Mateus Mondin, Antonio Augusto Franco Garcia, Margarida L R Aguiar-Perecin","doi":"10.1007/s00122-025-04862-7","DOIUrl":"https://doi.org/10.1007/s00122-025-04862-7","url":null,"abstract":"<p><strong>Key message: </strong>The influence of maize B chromosomes on flowering time was investigated, revealing a tendency for male flowering time to be delayed with an increase in the number of B chromosomes. This research aimed to verify whether the presence of B chromosomes alters the female and male flowering time of Zea mays L. For this purpose, four experiments were carried out, three with inbred lines of the Zapalote Chico race and the last one with the hybrid Cateto x Zapalote Chico. These experiments consisted of classes differing in the number of B chromosomes and were designed in complete randomized blocks, with two replications. In the three experiments conducted with the inbred lines of the Zapalote Chico race, it was observed that B chromosomes had a minimal influence on female flowering. For male flowering time, the statistical analysis results indicated that at least part of the observed variation in the flowering time could be attributed to differences in the number of extranumerary chromosomes. The analysis of the Cateto x Zapalote Chico hybrid confirmed the results observed in the inbred lines of Zapalote Chico race, showing that the influence of B chromosomes on the flowering time in Zea mays L. was more pronounced in the male flowering time. The mechanism by which B chromosomes alter flowering time is still unknown, and more research is needed to better clarify the possible role that the euchromatic and heterochromatic regions of the extranumerary chromosomes may play on the flowering time of Zea mays L.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 4","pages":"73"},"PeriodicalIF":4.4,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143626082","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 large-scale multi-environment study dissecting adult-plant resistance haplotypes for stripe rust resistance in Australian wheat breeding populations.","authors":"Natalya Vo Van-Zivkovic, Eric Dinglasan, Jingyang Tong, Calum Watt, Jayfred Goody, Daniel Mullan, Lee Hickey, Hannah Robinson","doi":"10.1007/s00122-025-04859-2","DOIUrl":"10.1007/s00122-025-04859-2","url":null,"abstract":"<p><strong>Key message: </strong>Genetic variation in stripe rust resistance exists in Australian wheat breeding populations and is environmentally influenced. Stacking multiple resistance haplotypes or using whole-genome approaches will improve resistance stability and environmental specificity. Wheat stripe rust (Puccinia striiformis) is a fungal disease responsible for substantial yield losses globally. To maintain crop productivity in future climates, the identification of genetics offering durable resistance across diverse growing conditions is crucial. To stay one-step ahead of the pathogen, Australian wheat breeders are actively selecting for adult-plant resistance (APR), which is considered more durable than seedling resistance. However, deploying resistance that is stable or effective across environments and years is challenging as expression of underling APR loci often interacts with environmental conditions. To explore the underlying genetics and interactions with the environment for stripe rust resistance, we employ haplotype-based mapping using the local GEBV approach in elite wheat breeding populations. Our multi-environment trial analyses comprising 35,986 inbred lines evaluated across 10 environments revealed significant genotype-by-environment interactions for stripe rust. A total of 32 haploblocks associated with stripe rust resistance were identified, where 23 were unique to a specific environment and nine were associated with stable resistance across environments. Population structure analysis revealed commercial or advanced breeding lines carried desirable resistance haplotypes, highlighting the opportunity to continue to harness and optimise resistance haplotypes already present within elite backgrounds. Further, we demonstrate that in silico stacking of multiple resistance haplotypes through a whole-genome approach has the potential to substantially improve resistance levels. This represents the largest study to date exploring commercial wheat breeding populations for stripe rust resistance and highlights the breeding opportunities to improve stability of resistance across and within target environments.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 4","pages":"72"},"PeriodicalIF":4.4,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11906565/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143626076","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 candidate genes associated with resistance to aflatoxin production in peanut through genetic mapping and transcriptome analysis.","authors":"Dongxin Huai, Li Huang, Xiaomeng Xue, Bolun Yu, Yingbin Ding, Gaorui Jin, Hao Liu, Manish K Pandey, Hari Kishan Sudini, Huaiyong Luo, Xiaojing Zhou, Nian Liu, Weigang Chen, Liying Yan, Yuning Chen, Xin Wang, Qianqian Wang, Yanping Kang, Zhihui Wang, Xiaoping Chen, Huifang Jiang, Yong Lei, Boshou Liao","doi":"10.1007/s00122-025-04822-1","DOIUrl":"https://doi.org/10.1007/s00122-025-04822-1","url":null,"abstract":"<p><strong>Key message: </strong>Two major QTLs qAftA07and qAftB06.2 for peanut aflatoxin production resistance were identified and candidate genes for them were predicted. Peanut (Arachis hypogaea L.) is a globally significant oil and economic crop, serving as a primary source of edible oil and protein. Aflatoxin contamination is a main risk factor for peanut food safety and industry development worldwide. The most cost-economic and effective control strategy entails the exploration and utilization of natural resistance in peanut, alongside the development of resistant varieties. However, the underlying mechanism of resistance to aflatoxin production (AP) in peanuts remains elusive. In this study, a RIL population derived from a cross between Zhonghua 10 (susceptible) and ICG 12625 (resistant), was used to identify quantitative trait loci (QTLs) for AP resistance. Overall, seven QTLs associated with AP resistance were mapped on five chromosomes, explaining 6.83-17.86% of phenotypic variance (PVE). Notably, only two major QTLs, namely qAftA07and qAftB06.2, were consistently detected across different environments with 6.83-16.52% PVE. To predict the candidate genes for AP resistance in qAftA07and qAftB06.2, the transcriptome analysis of seeds from parental lines inoculated with Aspergillus flavus were conducted. A total of 175 and 238 candidate genes were respectively identified in qAftA07 and qAftB06.2, encompassing genes with non-synonymous genomic variations as well as differentially expressed genes. Combined with the weighted gene co-expression network analysis, 10 and 11 genes in qAftA07 and qAftB06.2 were characterized showing a high correlation with aflatoxin content, thereby representing the most promising candidate genes within these two QTLs. These results provide valuable insights for future map-based cloning studies targeting candidate genes associated with AP resistance in peanut.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 4","pages":"71"},"PeriodicalIF":4.4,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143617104","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 dissection of flowering time and fine mapping of qFT.A02-1 in rapeseed (Brassica napus L.).","authors":"Yanling Li, Xin Li, Dezhi Du, Qianru Ma, Zhi Zhao, Long Wang, Yongshun Zhang, Huiqin Shi, Hongping Zhao, Huaxin Li, Damei Pei, Zhigang Zhao, Guoyong Tang, Haidong Liu, Haojie Li, Lu Xiao","doi":"10.1007/s00122-025-04845-8","DOIUrl":"https://doi.org/10.1007/s00122-025-04845-8","url":null,"abstract":"<p><strong>Key message: </strong>qFT.A02-1, a major quantitative trait locus controlling flowering time in Brassica napus, was mapped to a 104.8-kb region on chromosome A02, and BnaA02G0156900ZS is the candidate gene in response for flowering time. Flowering time is a key agronomic trait that determines the adaptability of crops to the environment and thus affects yields. The mechanism underlying flowering time is still far from clear in Brassica napus. In this study, a recombinant inbred line population composed of 215 lines was constructed and 35 flowering time QTLs were identified. One major QTL, qFT.A02-1 (explaining 16.40-17.80% of phenotypic variation), was detected in two environments, which was confirmed by QTL-seq. A residual heterozygous line containing qFT.A02-1 for flowering time was further constructed, and qFT.A02-1 was subsequently fine-mapped to a 104.8-kb interval, wherein a total of 11 genes were predicted. Candidate gene functional annotation implied that BnaA02G0156900ZS, a homologous gene of FLOWERING LOCUS T in B. napus, was likely the candidate gene for qFT.A02-1. HiFi sequencing of the two parents was subsequently conducted, and a 1,079-bp insertion in the promoter of BnaA02. FT was confirmed. The allelic variation analysis in a diversity of accessions identified another 6 SNPs existing in the non-coding region of BnaA02. FT and the 1,079-bp insertion in promoter region are closely associated with the flowering time in B. napus. Haplotype analysis indicated that the flowering time of Hap02 is significantly earlier than Hap01 and Hap04, and Hap05 is significantly earlier than Hap04. Yield-related trait analysis revealed that there are no significant differences in yield-related traits between the two near-isogenic lines based on the target locus. These results may advance our understanding of the mechanism underlying flowering time in B. napus.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 4","pages":"70"},"PeriodicalIF":4.4,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143606374","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":"Heterosis and hybrid breeding.","authors":"Antonio Augusto Franco Garcia, Matthias Frisch, Yiqun Weng, Rajeev Varshney, Mark Sorrells, David D Fang","doi":"10.1007/s00122-025-04834-x","DOIUrl":"https://doi.org/10.1007/s00122-025-04834-x","url":null,"abstract":"","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 4","pages":"69"},"PeriodicalIF":4.4,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143606376","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":"Meta genetic analysis of melon sweetness.","authors":"Galil Tzuri, Asaf Dafna, Ben Itzhaki, Ilan Halperin, Elad Oren, Tal Isaacson, Adi Faigenboim, Yelena Yeselson, Harry S Paris, Michael Mazourek, Joseph Burger, Arthur A Schaffer, Amit Gur","doi":"10.1007/s00122-025-04863-6","DOIUrl":"10.1007/s00122-025-04863-6","url":null,"abstract":"<p><strong>Key message: </strong>Through meta-genetic analysis of Cucumis melo sweetness, we expand the description of the complex genetic architecture of this trait. Integration of extensive new results with published QTL data provides an outline towards construction of a melon sweetness pan-QTLome. An ultimate objective in crop genetics is describing the complete repertoire of genes and alleles that shape the phenotypic variation of a quantitative trait within a species. Flesh sweetness is a primary determinant of fruit quality and consumer acceptance of melons. Cucumis melo is a diverse species that, among other traits, displays extensive variation in total soluble solids (TSS) content in fruit flesh, ranging from 2⁰ Brix in non-sweet to 18⁰ Brix in sweet accessions. We present here meta-genetic analysis of TSS and sugar variation in melon, using six different populations and fruit measurements collected from more than 30,000 open-field and greenhouse-grown plants, integrated with 15 published melon sweetness-related quantitative trait loci (QTL) studies. Starting with characterization of sugar composition variation across 180 diverse accessions that represent 3 subspecies and 12 of their cultivar-groups, we mapped TSS and sugar QTLs, and confirmed that sucrose accumulation is the key variable explaining TSS variation. All modes-of-inheritance for TSS were displayed by multi-season analysis of a broad half-diallel population derived from 20 diverse founders, with significant prevalence of the additive component. Through parallel genetic mapping in four advanced bi-parental populations, we identified common as well as unique TSS QTLs in 12 chromosomal regions. We demonstrate the cumulative less-than-additive nature of favorable TSS QTL alleles and the potential of a QTL-stacking approach. Using our broad dataset, we were additionally able to show that TSS variation displays weak genetic correlations with melon fruit size and ripening behavior, supporting effective breeding for sweetness per se. Our integrated analysis, combined with additional layers of published QTL data, broadens the perspective on the complex genetic landscape of melon sweetness and proposes a scheme towards future construction of a crop community-driven melon sweetness pan-QTLome.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 4","pages":"68"},"PeriodicalIF":4.4,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11897113/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143606390","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":"Genome-wide association mapping for the identification of stripe rust resistance loci in US hard winter wheat.","authors":"Rajat Sharma, Meinan Wang, Xianming Chen, Indira Priyadarshini Lakkakula, Paul St Amand, Amy Bernardo, Guihua Bai, Robert L Bowden, Brett F Carver, Jeffrey D Boehm, Meriem Aoun","doi":"10.1007/s00122-025-04858-3","DOIUrl":"10.1007/s00122-025-04858-3","url":null,"abstract":"<p><strong>Key message: </strong>The GWAS and testing with Yr gene linked markers identified 109 loci including 40 novel loci for all-stage and adult plant stage resistance to stripe rust in 459 US contemporary hard winter wheat genotypes. Stripe rust is a destructive wheat disease, caused by Puccinia striiformis f. sp. tritici (Pst). To identify sources of stripe rust resistance in US contemporary hard winter wheat, a panel of 459 Great Plains wheat genotypes was evaluated at the seedling stage against five US Pst races and at the adult plant stage in field environments in Oklahoma, Kansas, and Washington. The results showed that 7-14% of the genotypes were resistant to Pst races at the seedling stage, whereas 32-78% of genotypes were resistant at the adult plant stage across field environments, indicating the presence of adult plant resistance. Sixteen genotypes displayed a broad spectrum of resistance to all five Pst races and across all field environments. The panel was further genotyped using 9858 single-nucleotide polymorphisms (SNPs) generated from multiplex restriction amplicon sequencing (MRASeq) and the functional DNA markers linked to the known stripe rust resistance (Yr) genes Yr5, Yr15, Yr17, Yr18, Yr29, Yr36, Yr40, Yr46, and QYr.tamu-2B. A genome-wide association study (GWAS) was performed using genotypic and phenotypic data, which identified 110 SNPs and the functional markers linked to Yr15 and Yr17 to be significantly associated with stripe rust response. In addition, Yr5, Yr15, Yr17, Yr18, Yr29, and QYr.tamu-2B were detected by their functional DNA markers in the panel. This study identified 40 novel loci associated with stripe rust resistance in genomic regions not previously characterized by known Yr genes. These findings offer significant opportunities to diversify and enhance stripe rust resistance in hard winter wheat.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 4","pages":"67"},"PeriodicalIF":4.4,"publicationDate":"2025-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11893644/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143597796","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":"Characterization of a G. max × G. soja nested association mapping population and identification of loci controlling seed composition traits from wild soybean.","authors":"Linfeng Chen, Earl Taliercio, Zenglu Li, Rouf Mian, Thomas E Carter, He Wei, Chuck Quigely, Susan Araya, Ruifeng He, Qijian Song","doi":"10.1007/s00122-025-04848-5","DOIUrl":"10.1007/s00122-025-04848-5","url":null,"abstract":"<p><p>Wild soybean (Glycine soja Siebold & Zucc.) has valuable genetic diversity for improved disease resistance, stress tolerance, seed protein content and seed sulfur-containing amino acid concentrations. Many studies have reported loci controlling seed composition traits based on cultivated soybean populations, but wild soybean has been largely overlooked. In this study, a nested association mapping (NAM) population consisting of 10 families and 1107 recombinant inbred lines was developed by crossing 10 wild accessions with the common cultivar NC-Raleigh. Seed composition of the F₆ generation grown at two locations was phenotyped, and genetic markers were identified for each line. The average number of recombination events in the wild soybean-derived population was significantly higher than that in the cultivated soybean-derived population, which resulted in a higher resolution for QTL mapping. Segregation bias in almost all NAM families was significantly biased toward the alleles of the wild soybean parent. Through single-family linkage mapping and association analysis of the entire NAM population, new QTLs with positive allele effects were identified from wild parents, including 5, 6, 18, 9, 16, 17 and 20 for protein content, oil content, total protein and oil content, methionine content, cysteine content, lysine content and threonine content, respectively. Candidate genes associated with these traits were identified based on gene annotations and gene expression levels in different tissues. This is the first study to reveal the genetic characteristics of wild soybean-derived populations, landscapes and the extent of effects of QTLs and candidate genes controlling traits from different wild soybean parents.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 3","pages":"65"},"PeriodicalIF":4.4,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11889062/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143574113","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic dissection for seedling root-related traits using multiple-methods in bread wheat (Triticum aestivum L.).","authors":"Naicui Wei, Yuqiong Hao, Jinbo Tao, Jiajia Zhao, Bangbang Wu, Ling Qiao, Xiaohua Li, Xingwei Zheng, Juanling Wang, Jun Zheng","doi":"10.1007/s00122-025-04847-6","DOIUrl":"10.1007/s00122-025-04847-6","url":null,"abstract":"<p><strong>Key message: </strong>Several quantitative trait loci (QTL) and structural chromosome variations (SCVs) related to seedling root traits were identified using multiple methods, which provided valuable insights to assist breeding efforts in wheat. The root system of wheat affects water and fertilizer use efficiency, stress tolerance, and agronomic traits. Using association analysis and linkage mapping, QTL associated with 11 seedling-stage root traits were identified with single nucleotide polymorphisms (SNPs) and SCVs under both hydroponic nutrient solution culture experiment (NCE) and vermiculite culture experiment (VCE). Except for maximum root length (MRL), the root traits of seedlings under NCE and VCE differed significantly. Root fresh weight (RFW) and root dry weight (RDW) were significantly correlated with most agronomic traits and grain yield. Identification of RFW and RDW by NCE might provide a reference basis for VCE. Co-localization analysis revealed that NCE and VCE simultaneously detected SNP-loci viz. QRdw.sxau-6A, QRd.sxau-1B.2, and QDw.sxau-6A (5.56-8.76% of R²). The SCV-loci Mr1B-3, Mr3A-3 and Mr3A-4 were detected in both NCE and VCE (4.74-9.07% of R²). Furthermore, QRdw.sxau-6A, QSfw.sxau-6A and QRd.sxau-4A were detected using the mixed linear model (MLM), 3 Variance-component multi-locus random-SNP-effect Mixed Linear Mode (3VmrMLM) and rrBLUP. In the association panel, SNPs and SCVs co-localized to 14 MTAs, of which Mr5A-6 and QRd.sxau-5A were significantly associated with root diameter (RD). The association panel and doubled haploid (DH) population co-located 10 QTL, of which QDw.sxau-1D was stably detected. Finally, QDw.sxau-6A and Mg6A-9 overlapped in same genomic location containing candidate genes TraesCS6A02G372300, TraesCS6A02G382900 and TraesCS6A02G365100. The present study contributes novel insights into the genetics of root architecture in wheat.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 3","pages":"66"},"PeriodicalIF":4.4,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143574114","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}