Theoretical and Applied Genetics最新文献

{"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":"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":"Photosynthesis-informed breeding to enhance Soybean (Glycine max) yield potential: a framework integrating high-throughput phenomics, genomic prediction and G×E×M.","authors":"Harmeet Singh-Bakala, Francia Ravelombola, Caio Canella Vieira, Laavanya Rayaprolu, Matthew Herritt, Jacob D Washburn, Ru Zhang, Feng Lin, Grover Shannon","doi":"10.1007/s00122-026-05374-8","DOIUrl":"10.1007/s00122-026-05374-8","url":null,"abstract":"<p><strong>Key message: </strong>Unexploited genetic variation in soybean photosynthetic efficiency can be converted into yield gains by coupling high-throughput phenotyping with genomic-phenomic prediction within a G×E×M-oriented breeding framework built on heritable, physiologically meaningful traits. Improving crop yield through enhanced photosynthetic efficiency (PE) is a re-emerging and increasingly tractable objective for modern breeding, driven by recent advances in high-throughput field phenotyping, genomics, and data analytics. In C3 crops like soybean, radiation use efficiency (RUE) remains below the theoretical maximum, and evidence from cereals and legumes indicates that gains in RUE have contributed substantially to long-term yield improvement, suggesting unrealized potential in soybean. However, despite extensive physiological and genetic studies, PE has historically been difficult to integrate into breeding programs due to the complexity of photosynthetic processes and the historical lack of reliable high-throughput field-scale phenotyping and predictive breeding frameworks. This review synthesizes current knowledge on biological determinants of PE in soybean (leaf and canopy morphology, non-foliar photosynthesis), alongside natural genetic variation and the genetic architecture of photosynthesis (PS)-related traits. We summarize recent transgenic and functional studies that demonstrate the capacity to modify PS processes, while highlighting challenges of achieving durable yield benefits in real field conditions. We further review emerging high-throughput phenotyping (HTP) platforms, including unmanned aerial vehicles (UAVs)-assisted multi/hyperspectral imaging and ground-based portable sensors, that enable scalable assessment of PS-related traits across diverse field environments and management regimes. We argue that bridging the gap between photosynthetic potential and realized yield requires the integrating HTP with genomics, phenomic prediction and molecular breeding frameworks. We propose a pragmatic breeding pipeline that prioritizes standardized, biologically meaningful and heritable PE traits and proxy traits, leverages diverse germplasm for allele discovery, and applies integrated genomic-phenomic prediction frameworks that explicitly incorporate genotype × environment × management (G×E×M) interactions. By embedding PS-traits as complementary selection criteria within breeding pipelines, this multi-disciplinary approach offers a practical route to accelerate genetic gain and enhance soybean yield resilience.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"139 10","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13623791/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149082070","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 allelic diversification of flowering genes via CRISPR-Cas enables the development of multiple early-flowering soybean lines.","authors":"Manon Monfort, Norbert Brugière, Julie Calbry, Laurène Lacou, Frank Roeber, Fabien Nogué","doi":"10.1007/s00122-026-05400-9","DOIUrl":"10.1007/s00122-026-05400-9","url":null,"abstract":"<p><strong>Key message: </strong>CRISPR-Cas multiplex editing generated a broad range of early-flowering soybean lines, advancing flowering by up to four weeks under controlled long-day conditions and by approximately one to two weeks in a field trial. Soybean is a promising crop for European agriculture, but its cultivation area remains smaller than its potential. A major limitation to broader adoption in Europe is the restricted number of elite lines adapted to local environmental conditions, particularly the photoperiod encountered at higher latitude. At these latitudes, soybean must flower early to complete its growth cycle before the onset of harsh autumn conditions. In this project, we employed a CRISPR-Cas multiplex knockout strategy, to generate allelic diversity in the gene network controlling flowering time, with the aim of developing earlier flowering soybeans lines better suited to European high latitudes. This approach successfully produced earlier flowering varieties, with flowering advances of up to four weeks compared to the controls. Starting from maturity group (MG) I and MG III lines, we developed, within two generations, gene-edited early flowering soybean lines with estimated maturity ranges between MG 000 and MG 0. Greenhouse observations were supported by a field trial, in an MG II environment, where edited lines flowered approximately one to two weeks earlier than their respective parental controls. These results demonstrate that multiplex editing of flowering-time genes can rapidly generate targeted allelic diversity and a broad spectrum of flowering phenotypes within elite soybean backgrounds. These results provide valuable breeding material and a genotype/phenotype resource for subsequent evaluation of flowering-time adaptation across environments.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"139 10","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13623812/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149082045","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":"Discovery of a novel non-race-specific adult-plant resistance (APR) locus conferring stripe rust immunity in spelt wheat and its suppression in bread wheat.","authors":"Vincent Fetterley, Jasneet Singh, Jujhar S Gill, Samuel Holden, Meng Li, Jennifer Ens, Pierre J Hucl, Curtis J Pozniak, Gurcharn S Brar","doi":"10.1007/s00122-026-05386-4","DOIUrl":"10.1007/s00122-026-05386-4","url":null,"abstract":"<p><strong>Key message: </strong>A novel non-race-specific adult-plant resistance locus, QYr.cbl-5D, from spelt wheat confers near-immune resistance to stripe rust. The resistance conferred by QYr.cbl-5D is suppressed in bread wheat from an unknown suppressor. Adult-plant resistance (APR) genes provide durable, non-race-specific resistance against wheat rust diseases. We identified a novel APR locus in the spelt wheat cultivar CDC Silex that confers non-race-specific near-immune resistance to stripe rust. The trait segregates as a single dominant gene in the CDC Origin/CDC Silex spelt populations, and bulked segregant analysis sequencing (BSA-seq) mapped the locus, QYr.cbl-5D, to a 0.31 Mb interval on chromosome 5D, confirming monogenic inheritance. Interestingly, introgression into bread wheat suppresses this resistance, a pattern consistent with a dominant suppressor or another background-dependent modifier. We generated a scaffold-scale assembly of CDC Silex to annotate the locus and its flanking region on 5D. Within a ± 1 Mb interval flanking the QYr.cbl-5D peak, six genes were identified, of which five had no predicted function and one encodes a DnaJ/HSP-C2H2 zinc-finger fusion protein. Future work will aim to clone this APR and identify the molecular basis of its suppression in bread wheat. Linked SNPs from this region will enable marker-assisted selection to deploy this APR locus, providing a durable resistance resource to support sustainable wheat breeding and reduce reliance on fungicides.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"139 10","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149070017","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":"Allele variation at the Rdm3 locus conferring resistance to soybean southern stem canker.","authors":"M Habib Widyawan, James W Buck, Zenglu Li","doi":"10.1007/s00122-026-05381-9","DOIUrl":"10.1007/s00122-026-05381-9","url":null,"abstract":"<p><strong>Key message: </strong>Crockett and PI 398469 carry distinct resistance alleles at the Rdm3 locus for soybean southern stem canker, supported by progeny analysis, sequence variation, candidate gene expression profiling, and allele transmission patterns. Genetic resistance to southern stem canker (SSC) in soybean is predominantly conditioned by the Rdm3 locus on chromosome (Chr) 14. Resistance at this locus has been identified in 'Crockett' and PI 398469; however, the allelic relationship between these lines remains unresolved. This study aimed to determine whether SSC resistance in Crockett and PI 398469 is governed by the same or distinct alleles at the Rdm3 locus. Progeny analysis of a Crockett × PI 398469 recombinant inbred line (RIL) population identified recombinant lines with weaker resistance and broader phenotypic variation than either parent, indicating that recombination at the Rdm3 locus disrupted favorable allele combinations and generated unexpected SSC resistance phenotypes. Consistent with this, sequence analysis of two priority candidate genes, Glyma.14G023500 and Glyma.14G022600, revealed variation associated with resistance between Crockett and PI 398469, as well as among resistant and susceptible RILs. Expression profiling of these candidate genes further demonstrated genotype-dependent temporal patterns, suggesting distinct regulatory mechanisms underlying resistance conferred by Rdm3 alleles from Crockett and PI 398469. In addition, the resistance alleles differed in their transmission behavior, with segregation distortion and underrepresentation of the Crockett allele observed across breeding populations and germplasm pools. Pedigree analysis further indicated an atypical origin of the Crockett Rdm3 allele. These results demonstrate that Crockett and PI 398469 carry functionally distinct resistance alleles at Rdm3, confirming allelic variation at a major SSC resistance locus and providing insight into the effective deployment of Rdm3 resistance in soybean breeding.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"139 10","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13616858/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149069822","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":"Combining genomic prediction and multi-trait indices through stochastic simulations: do index type and deployment order affect genetic gain?","authors":"Roberto Fritsche-Neto, Lorena Gabriela Coelho Queiroz, Jesimiel Viana, Kajal Gupta, Kashish Grover, Júlio César DoVale","doi":"10.1007/s00122-026-05398-0","DOIUrl":"10.1007/s00122-026-05398-0","url":null,"abstract":"<p><p>Genomic selection (GS) has transformed plant breeding by enabling early selection and potentially reducing cycle length, but how to integrate GS with classical multi-trait selection indices remains unclear. We used stochastic simulations to compare seven strategies combining Smith-Hazel (SH), Pesek-Baker (PB), and empirical (EMP) indices with or without GS in a rice breeding program targeting increased grain yield (GY), reduced chalkiness rate (CR), and stable plant height (PH). Trait importance was set to 70% for GY, 15% for CR, and 15% for PH. After a phenotypic-selection burn-in phase, we simulated ten recurrent cycles and evaluated strategies using population mean, selection accuracy, and additive genetic variance over the years. We also considered scenarios with different breeding cycle lengths (GS-based: 3 years; Traditional: 5 years), but the same selection intensity per stage. Thus, PB provides the best balance in gain responses, in terms of both magnitude and direction, with one of the highest GY, the greatest reduction in CR, and PH stabilization. Accuracy and additive genetic losses were more pronounced when the phenotypically constructed index was used as a single target for genomic prediction, especially for CR and PH. Overall, trait-specific genomic prediction followed by index construction better preserved genetic information and produced responses more consistent with the multi-trait breeding objectives.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"139 10","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13616857/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149070082","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":"Transposon-mediated structural haplotypes at CsMYB60 are associated with peel coloration in cucumber.","authors":"Chen Chen, Juan Chen, Huiming Chen, Xiaohong Liu, Xiangyang Lu, Yun Tian, Geng Zhou","doi":"10.1007/s00122-026-05388-2","DOIUrl":"10.1007/s00122-026-05388-2","url":null,"abstract":"<p><strong>Key message: </strong>A previously unrecognized MULE1+MULE2 structural haplotype at CsMYB60 was identified and associated with mature peel coloration in cucumber. Peel color is a major commercial and physiological trait in cucumber (Cucumis sativus L.), yet our understanding of the underlying molecular mechanisms remains incomplete. Previous work has shown that the R2R3-MYB transcription factor CsMYB60 regulates flavonoid and proanthocyanidin biosynthesis in cucumber fruit spines. More recent evidence further implicates this gene in peel color variation via intronic Mutator-like element (MULE) insertions or premature stop codons identified in diverse germplasm. In the present study, we utilized a pair of near-isogenic lines, a yellow-peel inbred line (L14) and its white-peel mutant (L19), to minimize genetic background effects and precisely dissect the genetic basis of peel color variation. Through bulked segregant analysis combined with high-resolution fine mapping in segregating populations derived from these lines, the peel color locus was narrowed to a 121-kb interval on chromosome 4 harboring the R2R3-MYB transcription factor CsMYB60. Sequence comparison revealed that the L14 allele carries both the previously-characterized MULE1 insertion and a second nearby MULE2 insertion within the second intron of CsMYB60, whereas L19 retains only MULE1. During the peel color-transition stage, the MULE1 + MULE2 haplotype showed higher CsMYB60 transcript abundance than the MULE1-only haplotype in the near-isogenic materials examined. CRISPR/Cas9-mediated knockout of CsMYB60 in the L14 background abolished yellow pigmentation, demonstrating that CsMYB60 is required for yellow mature peel formation in this background. Together, these results identify a previously unrecognized MULE1 + MULE2 structural haplotype associated with distinct CsMYB60 transcript abundance and mature peel coloration. The causal regulatory contribution of MULE2 itself remains to be determined. The associated marker may facilitate tracking of this structural haplotype in relevant cucumber breeding materials.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"139 10","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149070096","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 study of diverse soybean [Glycine max (L.) Merrill] accessions for agronomic and seed composition traits in Rwanda.","authors":"Doreen Mutoni, Felix B Fritschi, Trupti Joshi, Kerry Clark, Jason Gillman, Kristin Bilyeu","doi":"10.1007/s00122-026-05383-7","DOIUrl":"10.1007/s00122-026-05383-7","url":null,"abstract":"<p><strong>Key message: </strong>This research explored the genetic basis of adaptation for soybean to the low-latitude but high-elevation production regions in Rwanda. Soybean [Glycine max (L.) Merrill] is an increasingly important crop in Rwanda; however, production remains constrained by limited availability of high-yielding, locally adapted cultivars. The varieties introduced through Rwanda's Crop Intensification Program were developed for other regions of sub-Saharan Africa and exhibit poor adaptation, delayed maturity and low productivity in Rwanda. This study evaluated diverse germplasm to support development of a national soybean breeding program. A total of 466 accessions representing maturity groups (MG) III-X were evaluated across six environments in Rwanda during 2017 and 2018. Trials were conducted in randomized complete block designs with three or two replications. Traits evaluated included flowering (R1), beginning pod (R3), maturity (R8), reproductive periods, plant height, single-row harvest weight, 100-seed weight and seed protein and oil content. Genotype and genotype-by-environment effects were highly significant (p < 0.001) for all traits, with strong correlations among phenology, plant height, reproductive period and seed composition. MG IV-VII accessions demonstrated full season adaptation to Rwanda's high-elevation environments. Genome-wide association analysis identified significant QTNs: for R1 (30), R3 (26), R8 (33), reproductive periods from R1-R8 (25) and R3-R8 (9), plant height (31), 100-seed weight (30), single-row harvest weight (29), protein (17) and oil (8). GDD-based traits yielded 21, 19, 30, 24 and 10 QTNs for GDD_R1, GDD_R3, GDD_R8, GDD_RP and RP_3, respectively, for 222 unique and a total of 342 QTNs. These findings provide potential markers for selection and a foundation for breeding high-yielding, adapted soybean cultivars for high-elevation, low-latitude agroecosystems.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"139 10","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13616022/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149064386","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":"Comparative evaluation of GWAS-prioritized SNP, SSR, and insertion-type structural variant marker panels for genomic prediction in soybean.","authors":"Xiaoyue Zhu, Ruixin Zhang, Changhong Guo, Yongjun Shu","doi":"10.1007/s00122-026-05397-1","DOIUrl":"10.1007/s00122-026-05397-1","url":null,"abstract":"<p><p>Soybean (Glycine max (L.) Merr.) is an important crop worldwide, and improving genomic prediction efficiency for complex traits is essential for soybean breeding. In this study, two public soybean datasets for drought tolerance (DT) and plant height (PH) were used to evaluate the predictive value of SNP, simple sequence repeat (SSR), and insertion-type structural variant (INS-SV) markers. Genome-wide markers were identified from whole-genome resequencing data and filtered for downstream analyses. GWAS-assisted marker prioritization was performed using five methods, including GLM, MLM, FarmCPU, fastGWA, and BOLT-LMM, and Top-K marker panels with different densities were evaluated using 12 genomic selection models. GWAS-prioritized marker panels generally outperformed random 5 K SNP panels and achieved comparable or improved prediction accuracy relative to the full-marker SNP GBLUP baseline within the internal validation framework. A marker density of 5 K provided a practical balance between prediction accuracy and marker number in the present datasets. The relative performance of combined-marker panels was trait- and GWAS-method-dependent, with small positive (Δr) values for some DT panels but negligible gains for PH. GBLUP and Bayesian regression models showed relatively stable performance. Overall, GWAS-assisted marker prioritization provides an efficient feature-selection strategy for soybean genomic prediction, whereas multi-type marker panels should be evaluated against a standard SNP reference on a trait- and method-specific basis.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"139 10","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149040843","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":"Identification of a candidate self-incompatibility locus in beet (Beta vulgaris).","authors":"Gil Yardeni, Thomas Holzweber, Juliane C Dohm, Heinz Himmelbauer","doi":"10.1007/s00122-026-05368-6","DOIUrl":"10.1007/s00122-026-05368-6","url":null,"abstract":"<p><strong>Key message: </strong>This study provides the first genomic evidence for a candidate self-incompatibility locus in beets (Beta vulgaris), identifying T2/S-RNase candidate genes and a complex S-locus on beet chromosome 2. A comparison of self-incompatible and self-compatible beet taxa reveals structural degeneration linked to mating system shifts. This work establishes a genomics-first framework for investigating self-incompatibility in understudied taxa and offers important implications for crop breeding and the evolution of plant reproductive systems. The majority of flowering plants maintain various mechanisms to prevent self-fertilization. One such mechanism, the genetic self-incompatibility (SI) system, exists in about half of angiosperms. SI systems have been described for only few taxa, as their diversity and lack of homology renders their study complicated. Yet, an RNase-based SI system (RSI) has emerged as widespread and possibly ancestral to eudicots. RSI has been recognized in at least six plant families and lately also in Caryophyllales. Here, we utilize the accumulated knowledge of RSI systems and high-quality genomic resources to investigate the presence of RSI in beet, Beta vulgaris. The genus Beta encompasses both self-compatible and self-incompatible taxa. We examined the genes of five beet genome assemblies to identify a candidate for the female component of RSI, a T2/S-RNase, and its corresponding candidate S-locus. A locus on beet chromosome 2 met our criteria, supported by phylogenetics data, sequence characteristics, and expression patterns that are unique to S-RNases. The candidate S-locus in Beta was highly repetitive with gene copy number variation observed in different cultivars. By comparing the candidate S-locus of B. vulgaris with that of the self-compatible wild beet B. patula, we hypothesize a potential link between reproductive modes and S-locus architecture. Our analysis suggests that S-RNase genes derived from an ancestral and highly conserved gene family are present and active in Beta, fulfilling a reproductive function. Employing a genomics-first approach, this work contributes insights into T2/S-RNase evolution and lays the groundwork toward elucidating SI in sugar beet and its relatives.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"139 10","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13601201/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149031424","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}