Theoretical and Applied Genetics最新文献

{"title":"Identification of candidate gene for the wheat powdery mildew resistance gene Pm40 by bulked segregant analysis coupled with whole-genome sequencing (BSA-seq).","authors":"Huai Yang, Shengfu Zhong, Chen Chen, Feiquan Tan, Peigao Luo","doi":"10.1007/s00122-026-05360-0","DOIUrl":"10.1007/s00122-026-05360-0","url":null,"abstract":"<p><strong>Key message: </strong>An NLR gene has been identified as the candidate for the powdery mildew resistance gene Pm40 in the 236.9-241.0 Mb interval on wheat chromosome 7B. Wheat powdery mildew severely threatens wheat production, while Pm40 is a durable and effective resistance gene against the disease. To accelerate the practical application and theoretical understanding of Pm40, the resistant parent PI672537 carrying Pm40, the susceptible parent L958, and their F₂ and F_2:3 populations were employed for genetic analysis. A total of 191.4, 191.9, 336.2, and 316.5 Gb of whole-genome sequencing data were obtained from PI672537, L958, and the resistant and susceptible bulked pools, respectively. In total, 3,879,037 single nucleotide polymorphism (SNP) markers were identified and used for mapping. The results of bulked segregant analysis combined with whole-genome sequencing (BSA-seq) revealed that Pm40 was narrowed down to a chromosomal region spanning 233.3-254.8 Mb on wheat chromosome 7B. Subsequent marker development and genetic analysis localized the Pm40 locus to a region of 236.9-241.0 Mb. Within this 4.1 Mb chromosomal region, 21 annotated genes were identified, among which only TraesCS7B03G0444100 and TraesCS7B03G0444300 were potentially associated with disease resistance. TraesCS7B03G0444100 encodes a RING-type zinc finger protein, whereas TraesCS7B03G0444300 encodes a nucleotide-binding leucine-rich repeat (NLR) protein. Sequence analysis revealed three nonsynonymous SNPs in the coding region of TraesCS7B03G0444300, resulting in amino acid substitutions. Furthermore, a kompetitive allele-specific polymerase chain reaction (KASP) found that one SNP marker (kasp-2) co-segregated with powdery mildew resistance. Collectively, these results suggested that TraesCS7B03G0444300 could be the candidate gene underlying Pm40. This study provided a valuable foundation for marker-assisted breeding and future functional characterization of Pm40-mediated resistance in wheat.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"139 9","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148841394","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 Gypsy LTR retrotransposon insertion in BrNYC1-A04 causes the stay-green phenotype by inhibiting chlorophyll b degradation in Chinese cabbage (Brassica rapa L. ssp. pekinensis).","authors":"Peng Tao, Zhichen Yue, Weijun He, Yue Feng, Jinwan Zhang, Juanli Lei, Biyuan Li","doi":"10.1007/s00122-026-05358-8","DOIUrl":"10.1007/s00122-026-05358-8","url":null,"abstract":"<p><strong>Key message: </strong>A Gypsy LTR retrotransposon insertion in BrNYC1-A04 causes the stay-green phenotype of Chinese cabbage via bulked segregant analysis sequencing, fine-mapping, and gene silencing analysis. The stay-green trait positively influences the postharvest quality of Chinese cabbage (Brassica rapa L. ssp. pekinensis), a leafy vegetable crop in the Brassicaceae family. This trait is typically caused by defects in chlorophyll degradation. In this study, we identified BraA04g008820.3C as a candidate gene associated with the stay-green phenotype in Chinese cabbage through BSA-seq and fine-mapping analyses. The gene was subsequently named BrNYC1-A04 due to its high homology to Arabidopsis thaliana AtNYC1 (At4G13250). Sequence analysis revealed that a Gypsy long terminal repeat (LTR) retrotransposon (RT) insertion in the first intron of BrNYC1-A04 disrupts normal splicing. This produces a premature termination codon in the mRNA of BrNYC1-A04 in the 5BTL (stay-green) line, resulting in a loss-of-function mutation. The BrNYC1-A04 mutation affects both chlorophyll b degradation and chloroplast structure by modulating chlorophyll b reductase activity. Under dark-induced senescence, the transcriptional expression of BrNYC1-A04 is regulated by BrORE1. Virus-induced gene silencing (VIGS) of BrNYC1-A04 in the wild-type line HN19-G significantly delayed chlorophyll b degradation. Based on the identification and functional verification of the Gypsy LTR-RT insertion in BrNYC1-A04, we propose a model for how the BrNYC1-A04 mutation inhibits chlorophyll b degradation and confers the stay-green trait in Chinese cabbage.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"139 9","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148832721","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":"Standardized microhaplotype databases and frameworks for assessing and mining crop genetic diversity.","authors":"Dongyan Zhao, Meng Lin, Cristiane H Taniguti, Alexander M Sandercock, Shufen Chen, Ebrahiem Babiker, Nahla V Bassil, E Charles Brummer, Jose Roberto Camacho, Warren Chatwin, Shu-Yun Chen, Shaun J Clare, Guilherme da Silva Pereira, Maria David, Simon Phillip Fraher, Michael Hardigan, Angelyn Hilton, Lillian M Hislop, Brian M Irish, Moctar Kante, Tae Hwa Kim, Chong-Wei Lee, Hannele Lindqvist-Kreuze, Jenyne Loarca, Po-Hsien Lu, Cesar Agusto Medina Culma, Jose Fabián Jiménez Morales, James Polashock, John H Price, Heathcliffe Riday, Deborah A Samac, Devinder Sandhu, Reuben Ssali, Ruth Mayela Castro Vásquez, Phillip A Wadl, Xinwang Wang, Seymour A Webster, Zhanyou Xu, G Craig Yencho, Craig T Beil, Moira J Sheehan","doi":"10.1007/s00122-026-05340-4","DOIUrl":"10.1007/s00122-026-05340-4","url":null,"abstract":"<p><strong>Keymessage: </strong>Standardized microhaplotype databases for eight diverse crops enable multiallelic analyses, comparative genetics, and breeding decisions. Microhaplotypes are short genomic segments that contain multiple tightly linked variants, providing multi-allelic data that can enhance genetic resolution compared to traditional biallelic single nucleotide polymorphism (SNP) markers. Here, we present the creation and utilization of separate microhaplotype databases for eight crop species representing diverse genome sizes, ploidy levels, and breeding systems. We developed a standardized, species-agnostic pipeline for processing, filtering, and databasing microhaplotypes generated using the DArTag targeted genotyping platform. To enhance user accessibility, we developed a no-code, user-friendly application, HapApp, that uses an R Shiny front-end interface to allow breeders and researchers to add unique, standardized microhaplotype identities from raw DArTag reports and iteratively update the existing crop-specific database with the newly discovered microhaplotypes. Selected case studies with these databases highlight the operational advantages of microhaplotypes, especially for challenging, highly heterozygous, or polyploid species. They offer an informative alternative to traditional biallelic SNP analyses for resolving population structures and improving linkage map ordering. This integrated framework provides a reproducible and scalable foundation for managing and exploiting microhaplotype data in plant breeding and genetic research, enabling robust cross-project comparisons and facilitating trait discovery in both simple and complex crop genomes, while enabling comparative genomics and cross-species functional transfer that accelerates genetic gains across all crop species.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"139 9","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13506570/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148819568","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":"Cross incompatibility restricting genome exchange and diversification of primary gene pool in plants: challenges and opportunities.","authors":"Mahendar Thudi, Yogesh Dashrath Naik, Uday Chand Jha, M S Sai Reddy, Manish Kumar Pandey, Reyazul Rouf Mir, Muraleedhar S Aski, Murukarthick Jayakodi, Venugopal Mendu, Naveen Puppala, P V Vara Prasad, Somashekhar M Punnuri, Henry T Nguyen","doi":"10.1007/s00122-026-05347-x","DOIUrl":"10.1007/s00122-026-05347-x","url":null,"abstract":"<p><strong>Key message: </strong>Crop wild relatives provide essential genetic diversity for improving crop resilience; however, pre- and post-zygotic barriers often restrict interspecific hybridization. Recent approaches enable their effective use in crop improvement programs. Crop wild relatives (CWR), closely related wild taxa of cultivated crops, offer a wealth of genetic diversity essential for developing traits to help crops adapt to the challenges of biotic and abiotic stresses. This diversity is critical to meet the increasing global demand for food, especially under the looming threat of climate change. However, crossing between individuals from different species often results in maladapted or inviable offspring due to pre- and post-zygotic barriers. Pre-zygotic barriers prevent successful pollen-stigma interactions and pollen tube growth, while post-zygotic barriers include hybrid embryo or endosperm failure and chromosome pairing issues, contributing to cross incompatibility (CI). These barriers restrict genome exchange and hinder the diversification of the primary gene pool in plants. Overcoming these barriers is a significant challenge. This review explores the diverse pre- and post-zygotic barriers in interspecific hybridization, emphasizing genetic factors related to CI. Additionally, this review highlights biotechnological approaches such as somatic hybridization and embryo rescue techniques, which are used to overcome these barriers. Through continued research and innovation, these barriers can be overcome, unlocking the full potential of CWR to address the evolving demands of global agriculture. Recent advances in synthetic biology now offer the possibility to reprogram reproductive barriers, turning CI into a controllable trait for hybrid development.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"139 9","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13506544/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148819529","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 study in a US soft winter wheat population reveals novel and known sources of resistance to the Septoria tritici blotch pathogen Zymoseptoria tritici.","authors":"Lamia Aouini, Rupesh Gaire, Steven Scofield, Gina Brown-Guedira, Mohsen Mohammadi, Stephen B Goodwin","doi":"10.1007/s00122-026-05324-4","DOIUrl":"10.1007/s00122-026-05324-4","url":null,"abstract":"<p><strong>Key message: </strong>GWAS of 337 soft winter wheat genotypes from a breeding program in Indiana, USA identified marker-trait associations that likely correspond with existing and novel resistances to Septoria tritici blotch disease. Septoria tritici blotch (STB), caused by the ascomycete fungus Zymoseptoria tritici, is a major disease of wheat worldwide. To find additional sources of resistance, genome-wide association (GWA) was used to analyze 337 soft winter wheat genotypes from Indiana, USA, by inoculating seedlings with two isolates of Z. tritici in a complete randomized design. Necrosis and pycnidia development were assessed at 14, 18 and 22 days post-inoculation, enabling the calculation of area under the disease progress curve (AUDPC) for each parameter. Adjusted necrosis and pycnidia AUDPC scores were compared with 14,341 high-quality SNPs in a GWA analysis using the FarmCPU and GAPIT CMLM models to identify markers associated with the resistance. Significant (p < 0.05) isolate × genotype interactions were identified, confirming that the phenotypic variation was caused by isolate-specific resistance genes. Overall, 12 marker-trait associations (MTAs) were identified with Z. tritici necrosis and pycnidia resistance. All mapped MTAs were isolate and necrosis/pycnidia specific. Distinct MTAs were mapped for necrosis and pycnidia on chromosome 6A, and for pycnidia on chromosomes 1A, 1D, 3B, 4A, 5B, 6A and 7A. MTAs on chromosomes 5B, 4A, 6A, and 1D likely corresponded with the known genes Stb1, Stb7, Stb15 and Stb19, respectively. MTAs on chromosomes 1A, 3B, 4A, 6A and 7A were not associated with previously known Stb genes and may be novel. Candidate genes near the marker locations have been identified for further investigations. The GWAS showed that Indiana soft winter wheat germplasm segregates for novel and known Stb genes and constitutes a valuable breeding resource for Z. tritici resistance.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"139 9","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-08-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148814077","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 prediction vs. gene-based crop models: a case study on rice trait prediction.","authors":"Jinhan Zhang, Weijie Tang, Hongwei Ma, Wenliang Yan, Ioannis N Athanasiadis, Shaoyuan Zhang, Leilei Liu, Bing Liu, Liujun Xiao, Yan Zhu, Weixing Cao, Yunhui Zhang, Liang Tang","doi":"10.1007/s00122-026-05342-2","DOIUrl":"10.1007/s00122-026-05342-2","url":null,"abstract":"<p><p>Conventional breeding for ideotypes in target environments remains challenging due to genotype-by-environment interactions and the genetic complexity of key agronomic traits. Traditional multi-environment field trials are costly and time-consuming, limiting rapid genetic gain. These challenges highlight the need for digital tools to support rice breeding. However, two major approaches, genomic prediction (GP) and gene-based crop models (GBCMs), have distinct advantages. In this study, a dataset derived from a natural rice population comprising 210 genotypes, genotyped with about 650,000 markers, rice dry matter, and yield across three environments, was used to develop two genomic prediction models, genomic best linear unbiased prediction (GBLUP) and a convolutional neural network (CNN), together with a gene-based crop modeling framework. The effectiveness of these models in predicting rice traits and assisting in breeding selection was subsequently evaluated. Prediction results indicated that biomass and yield could be effectively predicted by all models, with Normalized Root Mean Square Error (NRMSE) values ranging from 10.60% to 18.59% and 9.93% to 18.19%, respectively. In terms of predictive accuracy, parameter-based crop models achieved the highest predictive accuracy, although it was confined to theoretical simulations. This was followed by the GBCM and CNN, whereas the GBLUP exhibited the lowest performance. Furthermore, GGE biplot analysis revealed the predictions of the GBCM aligned more closely with field observations than those of the CNN, emphasizing the potential of GBCM as a practical surrogate for digital breeding. These results provide valuable insights into modeling genotype-by-environment interactions and support the development of data-informed breeding strategies for future rice improvement.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"139 9","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-08-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148814226","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":"Natural variation in WRKY53 confers cold tolerance at the booting stage between japonica and indica rice.","authors":"Jiangli Yang, Changhua Liu, Zhuo Chen, Tong Zhai, Xiaojie Tian, Qingyun Bu, Jiaqi Tang","doi":"10.1007/s00122-026-05339-x","DOIUrl":"10.1007/s00122-026-05339-x","url":null,"abstract":"<p><strong>Key message: </strong>Natural variation at the WRKY53-C518G SNP drives cold tolerance divergence between rice subspecies.  The japonica-specific WRKY53^518C allele, originating from Chinese wild rice and selected in temperate regions, confers cold tolerance by reducing GA repression to protect pollen fertility, and thus provides a valuable target for rice breeding. Cold tolerance at the booting stage (CTB), when inflorescence development begins, is a major factor limiting rice (Oryza sativa L.) productivity and geographical distribution. However, only a few cold-tolerance genes have been identified. We previously showed that WRKY53 regulates CTB by directly associating with the promoters of GA biosynthesis genes and transcriptionally repressing their expression in anthers. In this study, we demonstrate that natural variation in WRKY53 contributes to CTB divergence between japonica and indica subspecies. We identify a functional SNP in the coding region (C518G) that underlies this variation: the japonica-associated WRKY53^518C allele confers stronger cold tolerance than the indica-prevalent WRKY53^518G allele. Mechanistically, WRKY53^518G exhibits higher transcriptional repression activity of GA biosynthesis compared to WRKY53^518C, leading to reduced anther GA content and impaired pollen development under low temperature. Population and geographic distribution analyses reveal that the WRKY53^518C allele likely originated in Chinese wild rice, was retained in temperate japonica during domestication, and subsequently spread to high-latitude regions, contributing to latitudinal adaptation in rice. Collectively, our findings establish WRKY53 as a key regulator of CTB and highlight the WRKY53^518C allele as a valuable genetic resource for enhancing cold tolerance in rice breeding.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"139 9","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148808848","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 mapping identifies QTL and candidate genes including Mendel's A gene controlling high levels of partial resistance to Fusarium avenaceum in Pea.","authors":"Stephen O Awodele, Krishna K Gali, Bunyamin Tar'an, Sabine Banniza, Syama Chatterton, Ambuj B Jha, Martine Jean, Navajeet Chakravarthy, Lachagari V B Reddy, Thomas D Warkentin","doi":"10.1007/s00122-026-05316-4","DOIUrl":"10.1007/s00122-026-05316-4","url":null,"abstract":"<p><strong>Key message: </strong>Fav-Ps2.1 is the first major QTL reported for Fusarium avenaceum resistance in pea and co-localizes with Mendel's A gene and putative resistance genes. A novel moderate-effect QTL Fav-Ps5.1 and one epistatic locus, independent of the A gene, were also reported. Flavonoid compounds associated with resistance to this pathogen were identified. Fusarium avenaceum, a necrotrophic soil-borne pathogen, is a member of the root rot pathogen complex posing a major threat to pea yield and quality worldwide. Strong resistance to Fusarium root rot (FRR) in pea is associated with seed coat and flower pigmentation, controlled by Mendel's A locus regulating anthocyanin biosynthesis. It is not clear whether the A locus is acting alongside resistance genes to confer high levels of resistance or whether alternative genetic pathways exist in pea cultivars. In this study, a pea recombinant inbred line population of 160 lines called PR-20 (AA×aa), polyphenolic profiles, and the pea reference genome were leveraged to understand the genetic control of Fusarium avenaceum resistance. Two novel quantitative trait loci (QTLs) including a major QTL Fav-Ps2.1 (41-42.2 cM) on chromosome 6 with 95% phenotypic variance explained (PVE), a moderate-effect QTL Fav-Ps5.1 (126-134 cM) on chromosome 3 with 9% PVE, and a putative epistatic interaction with 15% PVE, associated with resistance to F. avenaceum were identified. Both the epistatic region and Fav-Ps5.1 are anthocyanin pigment-independent. Fav-Ps5.1 is co-localized with many defense-response and flavonoid-related genes including NDR1/HIN1-like protein, WDR, MYB111, WRKY, Chitinase, PAL1, F-box/LRR-repeat protein, E3 ubiquitin-protein ligase PUB22, ABC transporters, and probable ethylene response sensor 1. Fav-Ps2.1 is co-localized with 35 disease resistance-related genes and overlaps with the A locus, which may explain the high PVE. A 'pea tobacco mosaic virus (TMV) resistance N-like protein' gene, encoding TIR-LRR domains, marks the peak of Fav-Ps2.1 at ~ 0.12 cM upstream of the A locus. Regression analysis with whole seed polyphenolic compounds in randomly selected 14 PR-20 lines including the parents showed that some colorless flavonoids (anthocyanin precursors), encoded by genes other than A, explained more variation in disease resistance (R² = 87-99%; P ≤ 0.001), compared to the A gene-encoding anthocyanin compounds (R² = 38-86%; P ≤ 0.018). Our results demonstrate that high FRR resistance is not determined only by the A locus but emerges from multiple coordinated resistance loci. These findings provide new insights into the genetic basis of F. avenaceum resistance for breeding FRR resistance in white-flowered pea varieties.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"139 9","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13499788/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148798066","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":"Bridging germplasm and mechanisms: screening for resistance and decoding defense strategies against rice gall midge (Orseolia oryzae Wood-Mason) in rice.","authors":"Fugang Huang, Xiaolin Li, Zhe Jiang, Huayu Huang, Shahzad Ahmad, Shuolei Liao, Jieli Wei, Jiawang Peng, Xiaohui Zhong, Zuyu Liao, Jingying Li, Yifan Huang, Biqiu Wu, Danting Li, Yongfu Qiu","doi":"10.1007/s00122-026-05350-2","DOIUrl":"10.1007/s00122-026-05350-2","url":null,"abstract":"<p><strong>Key message: </strong>From 4006 rice accessions, this study identified 20 highly resistant accessions against the rice gall midge and revealed that their resistance is closely associated with morphological and physiological traits, thus providing critical and diverse resources and insights for resistance breeding. The Asian rice gall midge (RGM, Orseolia oryzae Wood-Mason) is a major rice pest causing substantial yield losses. Its larvae parasitize basal meristematic tissues of rice shoots, inducing hollow, tube‑like galls known as \"silver shoots.\" Host plant resistance represents the most viable and economical strategy for managing this pest. However, resistant germplasm resources remain limited, and the mechanisms underlying resistance are still poorly characterized. In this study, we evaluated 4,006 natural rice accessions for RGM resistance using a bulk seedling screening assay. Based on resistance levels, the accessions were classified as follows: 20 (0.5%) highly resistant, 48 (1.2%) resistant, 78 (1.9%) moderately resistant, 451 (11.3%) susceptible, and 3,409 (85.1%) highly susceptible. Despite their high resistance, most of the 20 highly resistant accessions showed considerable genetic diversity and undesirable agronomic traits. Analysis of resistance mechanisms revealed that 11 accessions exhibited both antixenosis and antibiosis, while four and five displayed only antixenosis or only antibiosis, respectively. Thirteen of the highly resistant accessions resisted RGM through a non‑hypersensitive pathway. Morphological rice seedling traits at the three-leaf stage, particularly the angle and sheath height of the second leaf, were significantly correlated with RGM oviposition preference, as validated using natural populations and an F₂ segregating population, suggesting a role in antixenosis. Physiological comparisons showed markedly higher total phenolic and hemicellulose contents in shoots of resistant accessions than in susceptible ones. This study significantly expands the genetic resources for breeding RGM‑resistant rice and advances understanding of rice-RGM interactions, providing valuable insights and tools for crop improvement.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"139 9","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148798081","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 stability of fatty acid composition in sunflower oil is dependent on environment and affected by structural variation.","authors":"Markus Ingold, Qingming Gao, Jennifer R Mandel, James P McNellie, Kyle G Keepers, Jessica G Barb, John M Burke, Loren H Rieseberg, Brent S Hulke","doi":"10.1007/s00122-026-05346-y","DOIUrl":"10.1007/s00122-026-05346-y","url":null,"abstract":"<p><p>In sunflower (Helianthus annuus L.), the composition of fatty acids in the seeds, primarily oleic, linoleic, stearic and palmitic acid, is of utmost importance for oil quality. Despite this, the genetic basis of this trait and its interaction with the environment is poorly understood. Understanding this interaction is critical to improvement of sunflower within the context of climate change. In this work, we incorporated fatty acid composition measurements from the sunflower SAM population and eight environments across an extensive geographic cline into GWAS. The SAM panel consists of 287 varieties representing approximately 90% of sunflower diversity, for which 2.2 million high-quality SNPs with a MAF > 5% are available. For increased power, multivariate GWAS was performed with four different inputs: (i) mean fatty acid composition within each environment, (ii) mean fatty acid composition within each environment omitting high oleic varieties, (iii) trait stability within environments quantified by standard errors among replicate samples (α stability) and (iv) Eberhart and Russell's β, which quantifies trait stabilities across environments (β stability). All four analyses yielded highly significantly associated SNPs. We found that high oleic varieties exhibited high β trait stability, resulting in substantial overlap in markers between analyses (i) and (iv), with signals being fairly consistent between environments in analysis (i). For analyses (ii) and (iii), significant markers tended to vary between trials. For significant SNPs across all analyses, 147 candidate genes were identified, including promising candidates such as 15 fatty acid metabolism genes, 6 heat shock proteins and 22 transcription factors. Lastly, a large introgression consisting of two flanking inverted sequences on Chromosome 5 was found to coincide with α stability in the Georgia trial, suggesting a role in FA composition stability under high heat conditions.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"139 9","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13493422/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148798090","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}