Theoretical and Applied Genetics最新文献

{"title":"Tm-1 back in business: an allele from Solanum pennellii accessions plays a major role in ToBRFV resistance.","authors":"Romanos Zois, Mireille van Damme, Martin Verbeek, Luuk D H Veenendaal, Yuling Bai, Anne-Marie A Wolters","doi":"10.1007/s00122-025-05036-1","DOIUrl":"10.1007/s00122-025-05036-1","url":null,"abstract":"<p><strong>Key message: </strong>The Tm-1 allele from Solanum pennellii accessions together with an additional, likely recessive, locus are required for complete ToBRFV resistance. The Tobamovirus Tomato Brown Rugose Fruit Virus (ToBRFV) poses a significant threat to global tomato production. ToBRFV is a mechanically transmitted virus containing a single-stranded positive sense RNA genome. Disease symptoms include brown, rough patches on fruit surfaces, leaf mosaicism and shape abnormalities, and, in advanced stages, total collapse of infected plants. ToBRFV was first detected in the Middle East in 2014 and has rapidly spread to multiple countries across Asia, Europe, and America. In recent years, numerous studies have focused on the identification of ToBRFV resistance traits that are suitable for tomato breeding programs. In this study, we identified five ToBRFV-resistant accessions of Solanum pennellii, a wild relative of cultivated tomato. We confirmed that the major gene controlling this resistance trait is the S. pennellii allele of Tm-1. Tm-1 was previously identified in S. habrochaites as a semidominant Tomato Mosaic Virus (ToMV) resistance gene. Our results show that full resistance to ToBRFV disease requires an additional undescribed locus. These results show the potential of S. pennellii as a novel source of resistance against ToBRFV.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 10","pages":"248"},"PeriodicalIF":4.2,"publicationDate":"2025-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12432084/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145055918","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":"Assessment of genomic prediction capabilities of transcriptome data in a barley multi-parent RIL population.","authors":"Christopher Arlt, Delphine van Inghelandt, Jinquan Li, Benjamin Stich","doi":"10.1007/s00122-025-05029-0","DOIUrl":"10.1007/s00122-025-05029-0","url":null,"abstract":"<p><strong>Key message: </strong>Low-cost and high-throughput RNA sequencing data for barley RILs achieved GP performance comparable to or better than traditional SNP array datasets when combined with parental whole-genome sequencing SNP data. The field of genomic selection (GS) is advancing rapidly on many fronts including the utilization of multi-omics datasets with the goal of increasing prediction ability and becoming an integral part of an increasing number of breeding programs ensuring future food security. In this study, we used RNA sequencing (RNA-Seq) data to perform genomic prediction (GP) on three related barley RIL populations. We investigated the potential of increasing prediction ability by combining genomic and transcriptomic datasets, adding whole-genome sequencing (WGS) SNP data, functional annotation-based filtering, and empirical quality filtering. Our RNA-Seq data were generated cost-efficiently using small-footprint plant cultivation, high-throughput RNA extraction, and Library preparation miniaturization. We also examined sequencing depth reduction as an additional cost-saving measure. We used fivefold cross-validation to evaluate the prediction ability of the gene expression dataset, the RNA-Seq SNP dataset, and the consensus SNP dataset between the RNA-Seq and parental WGS data, resulting in prediction abilities between 0.73 and 0.78. The consensus SNP dataset performed best, with five out of eight traits performing significantly better compared to a 50K SNP array, which served as a benchmark. The advantage of the consensus SNP dataset was most prominent in the inter-population predictions, in which the training and validation sets originated from different RIL sub-populations. We were therefore able to not only show that RNA-Seq data alone are able to predict various complex traits in barley using RILs, but also that the performance can be further increased with WGS data for which the public availability will steadily increase.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 10","pages":"247"},"PeriodicalIF":4.2,"publicationDate":"2025-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12423136/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145034165","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":"On the origin of the late-flowering ppd-H1 allele in barley.","authors":"Rajiv Sharma, Salar Shaaf, Kerstin Neumann, Peter Civan, Yu Guo, Martin Mascher, Michal David, Adnan Al-Yassin, Hakan Özkan, Tom Blake, Sariel Hübner, Nora P Castañeda-Álvarez, Stefania Grando, Salvatore Ceccarelli, Michael Baum, Andreas Graner, George Coupland, Klaus Pillen, Ehud Weiss, Ian J Mackay, Wayne Powell, Benjamin Kilian","doi":"10.1007/s00122-025-04981-1","DOIUrl":"10.1007/s00122-025-04981-1","url":null,"abstract":"<p><p>To breed for climate resilient crops, an understanding of the genetic and environmental factors influencing adaptation is critical. Barley provides a model species to study adaptation to climate change. Here we present a detailed analysis of genetic variation at a major photoperiod response locus and relate this to the domestication history and dispersal of barley. The PPD-H1 locus (a PSEUDO-RESPONSE REGULATOR 7) promotes flowering under long-day conditions, and a natural mutation at this locus resulted in a recessive, late-flowering ppd-H1 allele. This mutation proved beneficial in high-latitude environments such as Northern Europe, where it allows extended vegetative growth during long spring days. We infer the origin of the mutated late-flowering ppd-H1 allele by re-sequencing a large geo-referenced collection of 942 Hordeum spontaneum, 5 Hordeum agriocrithon and 1110 domesticated (Hordeum vulgare) barleys. We demonstrate that the late-flowering phenotype originated from Desert-type wild barley in the Southern Levant and present evidence suggesting a post-domestication origin of the mutated ppd-H1 allele.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 10","pages":"246"},"PeriodicalIF":4.2,"publicationDate":"2025-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12423146/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145034170","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":"Resolving a century-old enigma: potato 'Bolters' originate from instability of the StCDF1.3 allele.","authors":"Corentin R Clot, Ron G M van der Hulst, Herman J van Eck","doi":"10.1007/s00122-025-05030-7","DOIUrl":"10.1007/s00122-025-05030-7","url":null,"abstract":"<p><strong>Key message: </strong>Potato bolters are caused by excision of a transposon from the StCDF1.3 allele, resulting in a somatic mutant with late maturity. Somatic mutations during vegetative propagation can lead to novel genotypes, known as sports. In cultivated potato (Solanum tuberosum), a recurring sport type, called 'Bolters', is characterized by vigorous haulms and prolonged flowering. Bolters emerge spontaneously during potato cultivation. While deviating phenotypes are typically rogued during clonal propagation, certain bolters have been selected as sub-clonal strains. Their delayed maturity results in a longer growing season and higher yield, in particular when cultivated under short daylengths. Despite their prevalence and agronomical benefits, the genetic basis of bolters has remained unresolved 160 years after their first description in the literature. We investigated whether allelic variation at the StCDF1 locus, a central regulator of potato life cycle, underlies the bolter phenotype. We describe 34 bolters from eight cultivars. Bolters are isogenic with their parent varieties and carried new StCDF1 alleles. These arose from excision events of the Class II TIR transposon disrupting the StCDF1.3 allele conferring early maturity. Among the newly formed alleles, we predominantly identified StCDF1.2 variants, characterized by a 7-nucleotide insertion and associated with a mild effect on early maturity. We also found novel variants, including StCDF1.7, with a 6-nucleotide in-frame insertion, which appears to confer an even milder shortening of the life cycle. Based on this knowledge, we propose that selecting bolters represents a promising breeding strategy to expand the cultivation range of elite varieties and to enhance allelic diversity at a key regulatory locus.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 10","pages":"245"},"PeriodicalIF":4.2,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12420743/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145030524","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":"Fine mapping of the dominant female sterility gene and novel model of hybrid seed production in cabbage (Brassica oleracea L. var. capitata).","authors":"Wenjing Ren, Jinchao Si, Jiamin Li, Yiliao Feng, Yuankang Wu, Xinyu Zhao, Chunyu Jiang, Limei Yang, Mu Zhuang, Honghao Lv, Yong Wang, Jialei Ji, Xuehui Yao, Xilin Hou, Yangyong Zhang","doi":"10.1007/s00122-025-05002-x","DOIUrl":"10.1007/s00122-025-05002-x","url":null,"abstract":"<p><p>Hybrid breeding based on male sterility requires the removal of male parents, which is time- and labor-intensive; however, the use of female sterile male parent can solve this problem. In the offspring of distant hybridization between Brassica oleracea and Brassica napus, we obtained a mutant, 5GH12-279, which not only fails to generate gynoecium (thereby causing female sterility) but also has serrated leaves that could be used as a phenotypic marker in seedling screening. Genetic analysis revealed that this trait was controlled by a single dominant gene. Further analysis revealed that Bo2g005230, an orthologous gene of LATE MERISTEM IDENTITY1 (LMI1) in Arabidopsis, was predicted as the candidate gene and was renamed BoLMI1c. Sequence analysis revealed that homoeologous exchange (HE) occurred within the BoLMI1c gene body of 5GH12-279, which resulted in the generation of a novel fusion transcript. Two pairs of primers, N5230-1F/1R and N5230-2F/2R, were designed and successfully used for the identification of different genotypes of BoLMI1c. Transcriptome analysis revealed that BoLMI1c orchestrates the expression of several related biological processes and transcription factors. Furthermore, we found that self-pollination with mason bees produced no seeds in 5GH12-279, whereas the near-isogenic line 5GH12-170 produced seeds that were normal. Therefore, a new labor-saving hybrid seed production system with no need to remove the male parents, which is especially important for mechanized harvest in the future, has been proposed. Our study provides a valuable source of dominant female sterility and suggests the potential utilization of the female sterile line in hybrid breeding for mechanized harvest.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 10","pages":"244"},"PeriodicalIF":4.2,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12420705/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145030541","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":"Harnessing historical genebank data to accelerate pea breeding.","authors":"Lanique Niels, Jochen Christoph Reif, Lars-Gernot Otto, Vilson Mirdita, Markus Oppermann, Ulrike Lohwasser, Matthias Kotter, Stephan Weise, Samira El Hanafi","doi":"10.1007/s00122-025-05032-5","DOIUrl":"10.1007/s00122-025-05032-5","url":null,"abstract":"<p><p>The German Federal Ex Situ Genebank for Agricultural and Horticultural Crops (IPK) harbours over 3000 pea plant genetic resources (PGRs), backed up by corresponding information across 16 key agronomic and economical traits. The unbalanced structure and inconsistent format of this historical data has precluded effective leverage of genebank accessions, despite the opportunities contained in its genetic diversity. Therefore, a three-step statistical approach founded in linear mixed models was implemented to enable a rigorous and targeted data curation. Spring accessions revealed considerable breeding potential, with protein content exceeding market standards by almost one-fifth and with hundred grain weight that could match the upper limits reported for European elite varieties. This variation is embedded within structured populations, comprising five convarieties including sugar snaps and field pea, adding value for breeding across diverse morphotypes and market segments. Winter accessions demonstrated cold resilience, with post-winter survival rate up to 79.27% under minimum temperatures as low as - 17.1 °C. This variation is of particular relevance given the limited availability of winter-hardy cultivars able to evade summer drought and heat stresses. Transformation of the IPK Genebank into a bio-digital resource redirects formerly static material into central leverage for plant breeding in view of contemporary challenges. As such, this investigation activated the IPK pea population for use in among others breeding for a wide variety of ideotypes, research into adaptation, and future combination with omics studies.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 10","pages":"243"},"PeriodicalIF":4.2,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12420702/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145024263","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":"Optimising parent selection in plant breeding: comparing metaheuristic algorithms for genotype building.","authors":"S Yadav, S Dillon, M McNeil, E Dinglasan, R Mago, P Dodds, L Hickey, B J Hayes","doi":"10.1007/s00122-025-05028-1","DOIUrl":"10.1007/s00122-025-05028-1","url":null,"abstract":"<p><p>Stacking desirable haplotypes across the genome to develop superior genotypes has been implemented in several crop species. A major challenge in Optimal Haplotype Selection is identifying a set of parents that collectively contain all desirable haplotypes, a complex combinatorial problem with countless possibilities. In this study, we evaluated the performance of metaheuristic search algorithms (MSAs)-genetic algorithm (GA), differential evolution (DE), particle swarm optimisation (PSO), and simulated annealing (SA) for optimising parent selection under two genotype building (GB) objectives: Optimal Haplotype Selection (OHS) and Optimal Population Value (OPV). Using a diverse wheat population of 583 lines genotyped for 29,972 SNPs, forming 7645 haplotype blocks and phenotyped for stripe rust scores, we assessed each algorithm's performance across fitness optimisation, convergence speed, and computational efficiency. GA consistently achieved high fitness and rapid convergence, while DE showed robustness but required longer runtime and careful tuning. PSO performed well under the OHS criterion but was less effective for OPV. SA, although computationally lighter, was less consistent in finding optimal solutions. Simulation over 100 breeding cycles showed that OHS outperformed both OPV and GEBV-based selection in long-term genetic gain and diversity retention. OHS maintained heterozygosity and additive variance, which are key for sustainable improvement, while GEBV selection led to early allele fixation. Our findings underscore the potential of GB strategies that prioritise the collective performance of parent sets rather than individual ranking to enhance selection outcomes in genomic-assisted breeding programmes.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 9","pages":"242"},"PeriodicalIF":4.2,"publicationDate":"2025-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12414015/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145008501","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 identification of the SAM-dependent methyltransferase members and functional analysis of GmSAMMt30 in soybean (Glycine max) under salt-alkali stress.","authors":"Wenjing Zhang, Jinqi Yu, Zitian He, Jiaxuan Guo, Changchao Huang, Qingqing Xu, Xianya Dong, Ziyi Yang, Beixi Chen, Cheng Quan, Meiqing Li, Qi Zhang, Jidao Du","doi":"10.1007/s00122-025-04982-0","DOIUrl":"https://doi.org/10.1007/s00122-025-04982-0","url":null,"abstract":"<p><p>Saline-alkali soil poses a severe threat to the cultivation and yield of soybean, which is an important oilseed and staple crop. As a key metabolic intermediate, S-adenosyl-L-methionine (SAM) and its associated methyltransferases (SAMMTs) play crucial but poorly understood roles in plant stress responses. This study investigated the expression of SAM-depend methyltransferase (SAMMt) family in soybean. A total of 69 identified GmSAMMt members were divided into 13 subfamilies with similar gene structures by phylogenetic analysis. The GmSAMMt members contained cis-acting elements involved in abiotic stress responses, hormone regulation, and plant growth and development. A tissue-specific expression analysis identified 43 GmSAMMt members with high levels of expression. Haplotype analysis and quantitative real-time PCR (qRT-PCR) screening identified GmSAMMt30 as the most promising candidate gene responsive to saline-alkali stress. In yeast heterologous expression assays, compared to the control strain INVScI(pYES2), GmSAMMt30^Hap2 significantly enhanced the growth of recombinant yeast under saline-alkali stress, whereas GmSAMMt30^Hap1 exhibited markedly inhibited growth relative to GmSAMMt30^Hap2. In transgenic soybean hairy roots, the GmSAMMt30^Hap2 genotype showed significantly better phenotypic performance under salt-alkali stress than K599(pSOY1) with lower leaf wilting and content of reactive oxygen species (ROS). In contrast, the GmSAMMt30^Hap1 genotype showed increased sensitivity to salt-alkali stress, with more severe leaf wilting and a higher ROS content compared to K599(pSOY1). Therefore, the study lays the foundation for in-depth research on the soybean salt-alkali tolerance traits and its application in molecular marker-assisted breeding for this legume crop.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 9","pages":"240"},"PeriodicalIF":4.2,"publicationDate":"2025-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144993573","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":"Prediction of Australian wheat genotype by environment interactions and mega-environments.","authors":"Nick S Fradgley, Guillermo S Gerard, Velu Govindan, Julie M Nicol, Amit Singh, Wuletaw Tadesse, Alexander B Zwart, Richard Trethowan, Ben Trevaskis, Alex Whan, Jessica Hyles","doi":"10.1007/s00122-025-05023-6","DOIUrl":"10.1007/s00122-025-05023-6","url":null,"abstract":"<p><strong>Key message: </strong>Latent environmental effects of genotype by environment interactions could be predicted from observed environmental covariates. Predictions into the wider target population of environments revealed greater insights. Wheat is grown across a diverse range of environments in Australia with contrasting environmental constraints. Targeted breeding to optimise genotypes in target environments is hindered by large and ubiquitous genotype by environment interactions (GEI). Common GEI in multi-environment trial experiments, which sample the target population of environments, can be efficiently modelled using latent environmental effects from factor analytic mixed models. However, generalised prediction into the full target population of environments is difficult without a clear link to observed environmental covariates (ECs) that are defined from high-resolution weather and soil data. Here, we used a large wheat multi-environment trial dataset and demonstrated that latent environmental effects can be associated with and predicted from observed ECs. We found GEI-based environment classes could be defined by combinations of key ECs. Prediction of main and latent effects in a wider set of environments covering the full TPE across the Australian grain belt over 13 years revealed the complex trends of environmental effects and GEI over regional scales demonstrating high year-to-year variability. Regional environment types often shifted year-to-year. Cross-validation of forward genomic prediction into untested year environments demonstrated that increased accuracy is possible if estimated genetic effects are also accurate and ECs of new environments are known. These findings may guide Australian wheat breeders to better target specifically adapted material to mega-environments defined by static GEI while also considering broad adaptability and non-static GEI resulting from year-to-year variability.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 9","pages":"241"},"PeriodicalIF":4.2,"publicationDate":"2025-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12411322/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144993498","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":"Mutations in BrMYB31 lead to a glossy phenotype caused by a deficiency in epidermal wax crystals in Chinese cabbage.","authors":"Xinghua Qi, Jiaqi Zou, Xiaoli Tang, Jie Ren, Gengxing Song, Hui Feng","doi":"10.1007/s00122-025-05031-6","DOIUrl":"10.1007/s00122-025-05031-6","url":null,"abstract":"<p><strong>Key message: </strong>Mutations in BrMYB31 were responsible for glossy phenotype, which was verified in two allelic mutants and gene silencing analysis. BrMYB31 regulated wax biosynthesis by modulating BrCER4 expression in Chinese cabbage. Plant cuticular wax plays a crucial role in resisting both biotic and abiotic stresses, but its deficiency is beneficial for improving the commercial properties of certain leafy vegetables. The glossy appearance resulting from the absence of epidermal wax crystals is a striking product feature of Chinese cabbage (Brassica rapa L. ssp. pekinensis). In this study, we identified two allelic mutants with wax crystal deficiency (wdm2 and wdm5) derived from an ethyl methane sulfonate (EMS)-mutagenized population of Chinese cabbage. Genetic analysis indicated that a recessive nuclear gene is responsible for the glossy phenotype. Based on MutMap sequencing combined with the kompetitive allele-specific PCR (KASP) genotyping approach, BraA02g022420.3C, a gene belonging to MYB transcription factor family, was predicted as the candidate gene and designated it as BrMYB31. Allelic mutant sanger sequencing analysis revealed a single-nucleotide polymorphism (SNP) (G/A) in the 2nd exon of BrMYB31 in wdm2, resulting in the substitution of lysine (K) with arginine (R), and also a SNP (G/A) in the 3rd exon of BrMYB31 in wdm5, causing tryptophan (W) to be converted into a terminator (X). Further virus-induced gene silencing analysis demonstrated that suppression of BrMYB31 exhibited a glossy phenotype. Transcriptome analysis revealed that BrMYB31 likely regulates glossy leaf characteristics probably by impacting wax biosynthesis-related genes expression. Transcriptional activity assays confirmed that BrMYB31 functions as a transcriptional activator. Yeast one-hybrid assays, luciferase reporter assays, and GUS activity analyses indicated that BrMYB31 could directly bind to BrCER4 promoter. This study illustrates the effectiveness of integrating MutMap and KASP in mining candidate genes associated with glossy leaf traits in EMS mutants and provides new insights into the regulatory network of cuticle wax biosynthesis in Chinese cabbage.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 9","pages":"239"},"PeriodicalIF":4.2,"publicationDate":"2025-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144970163","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}