Plant Genome最新文献

{"title":"Multi-environment evaluation and genomic prediction of agronomic traits in the southern US rice genepool.","authors":"Mary-Francis LaPorte, Haixiao Hu, Walter Solomon, James H Oard, Steven J Knapp, Daniel E Runcie, Jeremy D Edwards, Anna McClung, Christine H Diepenbrock","doi":"10.1002/tpg2.70222","DOIUrl":"10.1002/tpg2.70222","url":null,"abstract":"<p><p>The southern United States is responsible for 80% of the country's production of rice, approximately half of which is exported. Understanding genotypic and environmental factors impacting the historical performance of rice (Oryza sativa L.) is important for directing research efforts to optimize production of this globally important crop. A set of 429 rice genotypes including globally diverse historical parents and advanced japonica breeding lines from southern US breeding programs was phenotyped in 2008 for eight agronomic traits in Arkansas, Louisiana, and Mississippi. They were also genotyped using a single-nucleotide polymorphism set optimized for genomic prediction/selection. Genotypic and phenotypic data were analyzed via clustering techniques and principal component analysis. Single-trait and multi-trait genomic prediction were used to predict genetic values on a per-plant basis. We found that contemporary germplasm from the southern state breeding programs was highly interrelated and distinct from progenitor indica and temperate japonica genotypes. Genomic predictive abilities were high and largely consistent across environments for seed number per panicle, tiller number, and plant height. Although predictive abilities were lower for seed weight per panicle, that trait was correlated with seed number per panicle (r = 0.919), and predictive ability was higher for both traits in a multi-trait prediction framework. Furthermore, including data from the two major genotypic clusters identified herein had no penalty on genomic predictive ability. The data and analyses presented herein could inform future genomic and phenotypic investigations and applied breeding in the southern US rice germplasm pool.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"19 2","pages":"e70222"},"PeriodicalIF":4.3,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13034092/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147575973","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of resistance sources and genomic regions regulating spot blotch resistance in Asian bread wheat (Triticum aestivum L.) via genome-wide association study.","authors":"Nikita Aggarwal, Xinyao He, Mukesh Rathore, Farkhandah Jan, Vikas Gupta, Reyazul Rouf Mir, Pawan K Singh","doi":"10.1002/tpg2.70228","DOIUrl":"10.1002/tpg2.70228","url":null,"abstract":"<p><p>Spot blotch (SB), caused by Bipolaris sorokiniana, is a major yield-limiting disease of wheat (Triticum aestivum L.) in the warm, humid agroclimatic zones of South Asia. The development of resistant cultivars through molecular approaches offers a sustainable strategy for managing this disease. This study aimed to identify resistant genotypes and associated single-nucleotide polymorphism markers in a panel of 187 spring bread wheat lines via field-based phenotyping and genome-wide association study (GWAS). The panel was genotyped via the DArTSeq genotyping-by-sequencing platform and evaluated for SB resistance under artificially inoculated field conditions across two crop seasons (2019-2020 and 2020-2021) at Agua Fria, Mexico. Significant phenotypic variation was observed, with genotypes BGD54, IND56, and BGD55 showing high levels of resistance, indicating their potential as resistance donors. GWAS identified multiple marker‒trait associations (MTAs) linked to SB resistance, with seven stable MTAs consistently detected across years and models, located on chromosomes 3D, 5A, 3B, and 1B, and explaining 3.86%-18.17% phenotypic variance. Most of these MTAs colocalized with previously reported genomic regions for SB resistance. In silico analysis revealed candidate genes within these regions encoding potassium transporters, zinc finger proteins, glutathione S-transferases, FBD domain proteins, leucine-rich repeats, protein kinases, dirigent proteins, and cytochrome P450 enzymes. The identified stable MTAs and associated candidate genes offer valuable resources for marker-assisted selection and functional validation in wheat breeding programs targeting SB resistance.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"19 2","pages":"e70228"},"PeriodicalIF":4.3,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13022948/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147533812","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"GWAS and genomic prediction of crown rust resistance in the southern US elite oat (Avena sativa L.) germplasm.","authors":"Janam Prabhat Acharya, Md Ali Babar, Kathy Esvelt Klos, Stephen Harrison, Noah DeWitt, Amir M H Ibrahim, Paul Murphy, Raja Sekhar Nandety, Jason Fiedler","doi":"10.1002/tpg2.70233","DOIUrl":"10.1002/tpg2.70233","url":null,"abstract":"<p><p>Crown rust (CR), caused by Puccinia coronata f. sp. avenae, is a major constraint to oat (Avena sativa L.) production in the southern United States. We dissected the genetic architecture of CR resistance and assessed genomic prediction in 234 winter and facultative oat lines adapted to the southern United States. Using multi-environment phenotyping across five CR-prone sites and 8,234 high-quality single-nucleotide polymorphisms, we conducted genome-wide association study (GWAS) and genomic prediction analyses. GWAS detected 13 significant loci, nine of which co-localized with reported quantitative trait loci  or contained plausible resistance candidates such as leucine-rich repeat (LRR), nucleotide-binding site-LRR, and serine/threonine kinases. A stable locus on chromosome 3D was repeatedly identified in Baton Rouge, LA (2016); Castroville, TX (2016); Winnsboro, LA (2017); and in the combined analysis, indicating cross-environment consistency. Additional loci were supported on chromosome 4C (Citra and Quincy, FL, in 2017, and the combined analysis) and 2A (Winnsboro, LA, in 2017 and the combined analysis). Allele stacking was associated with large phenotypic gains. Lines with five or more favorable alleles showed >56% lower crust and 63% lower Crust_Per than lines with none, supporting marker-assisted pyramiding. Genomic prediction models achieved high prediction accuracy. Parametric models, particularly BayesA and RRBLUP, performed strongly across cross-validation schemes; random forest was broadly comparable; and gradient boosting was lower. These results underscore the effectiveness of using GWAS and genomic prediction to enhance breeding for durable CR resistance in oat and provide a genomic framework for developing resilient cultivars suited to southern United States growing conditions.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"19 2","pages":"e70233"},"PeriodicalIF":4.3,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13034105/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147576028","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Missing comparability: When genomic selection faces field variability. A case study in soybeans.","authors":"Edmundo Caballero, Julian Garcia-Abadillo, Diego Jarquin","doi":"10.1002/tpg2.70264","DOIUrl":"10.1002/tpg2.70264","url":null,"abstract":"<p><p>The processing of phenotypic information prior to training genomic selection (GS) models is a key factor that is frequently overlooked. Several approaches have been proposed to isolate the genetic signal from the field variability. However, in most cases, the estimated genetic signal still carries the field variability print. In addition, the statistical metrics are not conclusive about the model that isolates the signal the best since the breeding values are unknown. In this study, we evaluate the effects of different spatial models for separating the genetic from the field variability components, and their repercussions implementing GS models. A real soybean (Glycine max L. Merr.) data and a simulation study under controlled conditions were analyzed. Three standard models were implemented accounting for different field variability components (M1: block, M2: block + row + column, and M3: block + row + column + row × column). Results derived from the real dataset showed that accounting for field variability reduces predictive ability of the isolated genetic signals. In the simulated data, however, it was found that field variability corrections improved the predictive ability of breeding values. We conclude that training GS models with isolated genetic signals improves the predictability of breeding values and that the current benchmarks, relying on the correlation between predicted and observed values, can be misleading due to the lack of comparability between phenotypes and breeding values.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"19 2","pages":"e70264"},"PeriodicalIF":4.3,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13261800/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148228902","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptome assemblies for two drug-type cannabis chemotypes by long-read RNA sequencing.","authors":"Oliver Berkowitz, Ricarda Jost, Sophia Ng, Antony Bacic, James Whelan, Mathew G Lewsey","doi":"10.1002/tpg2.70240","DOIUrl":"10.1002/tpg2.70240","url":null,"abstract":"<p><p>Cannabis sativa has undergone over 10,000 years of domestication, resulting in extensive genetic and phenotypic diversity among cultivated chemotypes. Increased medical and recreational use of specialized metabolites accumulating in cannabis glandular trichomes-primarily the cannabinoids ∆9-tetrahydrocannabinol (THC) and cannabidiol (CBD)-has amplified research interest and a need to develop supporting genomic tools. Here, we present PacBio Iso-Seq-based transcriptome assemblies for two contrasting cannabis drug-type chemotypes (THC- and CBD-dominant) and their characterization. These assemblies encompass approximately 60% of the annotated loci in the cs10 reference genome, consistent with the commonly expressed fraction of the genome, and identify 1145 novel transcribed loci not present in the cs10 reference. Each assembly defines >50,000 transcripts and 15,000 alternative splicing events. Their accuracy is exemplified by confirming the conservation of alternative splicing events for Rubisco activase and a serine/argine-rich protein (SR45). We further highlight their utility by characterizing a novel cis-regulatory long non-coding RNA associated with the transcription factor NITRATE REGULATORY GENE 2. In addition, alternative splicing events for SPX DOMAIN 4, a key regulator of phosphate homeostasis, identified expression of transcripts encoding proteins with altered domain structure. Quantification of transcript abundances of these genes across different organs and varying phosphate supplies revealed isoform-specific expression patterns that differ between chemotypes, suggesting novel regulatory mechanisms for nitrogen and phosphate acquisition not previously described in either model or crop plant species. Our transcriptome assemblies provide a rich resource for the functional characterization of transcript and protein diversity in cannabis.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"19 2","pages":"e70240"},"PeriodicalIF":4.3,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13071343/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147677997","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic architecture of phenological, morphological, and phytochemical traits in Cannabis landraces.","authors":"Mehdi Babaei, Davoud Torkamaneh","doi":"10.1002/tpg2.70243","DOIUrl":"10.1002/tpg2.70243","url":null,"abstract":"<p><p>Despite its long history of cultivation and diverse applications, Cannabis sativa remains underexplored at the genomic level, particularly in landrace populations that harbor untapped genetic diversity. In this study, we investigated the genetic architecture of 145 Iranian cannabis landrace accessions, including both male and female plants, using 233K common SNPs and genome-wide association studies. Our analysis revealed three genetically distinct subpopulations shaped by geography, climate, and traditional cultivation practices. We identified 91 significant genomic regions associated with 40 phenological, morphological, and phytochemical traits, including 15 key loci with pleiotropic effects linked to multiple traits, including flowering time, plant architecture, biomass accumulation, and cannabinoid biosynthesis. These findings highlight the complex interplay between developmental and metabolic pathways in cannabis. The high heritability of most traits and rapid linkage disequilibrium decay underscore the potential of these landraces for high-resolution mapping and genetic improvement. This work provides a valuable genomic resource for marker-assisted selection, supporting the development of improved cultivars with tailored cannabinoid profiles and agronomic traits.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"19 2","pages":"e70243"},"PeriodicalIF":4.3,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13155046/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147845006","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomics for next-generation wheat breeding.","authors":"Rajeev K Varshney, Vanika Garg, Manuel Spannagl, Susanne Dreisigacker","doi":"10.1002/tpg2.70263","DOIUrl":"10.1002/tpg2.70263","url":null,"abstract":"","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"19 2","pages":"e70263"},"PeriodicalIF":4.3,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13492579/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148158722","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide association studies of a pea germplasm reveal novel markers and candidate genes implicated in resistance to Fusarium oxysporum f. sp. pisi races 1 and 2.","authors":"Osman Zakaria Wohor, Diego Rubiales, Nicolas Rispail","doi":"10.1002/tpg2.70250","DOIUrl":"10.1002/tpg2.70250","url":null,"abstract":"<p><p>Pea (Pisum sativum L.) is an essential legume crop cultivated globally as food and feed. However, its production is greatly constrained by Fusarium oxysporum f. sp. pisi (Fop). Breeding for resistance is the most efficient management strategy, but the genetic foundation of Fop resistance remains unclear. Previous quantitative trait loci mapping has located several genomic regions associated with resistance to Fop. However, the large marker-trait distances hampered the implementation of marker-assisted selection. To unravel candidate genes for Fop races 1 and 2, diversity array technology (DArT) markers were applied to 324 pea core collections for a genome-wide association study (GWAS). Phenotyping of the collections were performed under controlled growth chamber conditions with three independent experiments in a 324 × 3 × 7 factorial design. The collections were inoculated, and disease incidence was quantified over time using the area under the disease progress curve as the primary phenotypic measure for analyses. Phenotypic results revealed quantitative response and implicated wild accessions and landraces as favorable reservoirs of Fop resistance. GWAS using 26,045 DArT markers with three different models detected 15 marker-trait associations (MTAs) for Fop race 1 and 27 MTAs for Fop race 2 resistance. MTAs were scattered across six pea chromosomes, with several of them located within the confidence interval of four previous Fop resistance loci-thereby refining their location. In addition, 28 potential candidate genes were identified near associated markers involved in Fop resistance, including genes encoding a reverse transcriptase, exocyst and conserved oligomeric Golgi complex subunits, a FERONIA-like receptor kinase, homoserine kinase, a heat shock 70 protein, adenosine triphosphate transporters, and multiple transcription factors and plant defense-related proteins. These putative genes and molecular pathways provide a foundation for the sustainable management of Fop.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"19 2","pages":"e70250"},"PeriodicalIF":4.3,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13492620/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147989799","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic identification and characterization of novel loci for flag leaf morphology traits in Chinese endemic wheat.","authors":"Md Nahibuzzaman Lohani, Longxing Su, Lu Lu, Li Yin, Yanlin Liu, Qiang Xu, Yunfeng Jiang, Qiantao Jiang, Guoyue Chen, Yuming Wei, Chunji Liu, Quan Xie, Jian Ma","doi":"10.1002/tpg2.70245","DOIUrl":"10.1002/tpg2.70245","url":null,"abstract":"<p><p>Flag leaf morphology (FLM) is a critical determinant of wheat (Triticum aestivum L.) photosynthetic efficiency and grain yield. Chinese endemic wheat, a unique genetic reservoir formed by long-term adaptation to diverse and heterogeneous environments in China, harbors abundant, untapped allelic variation for traits related to environmental resilience and yield architecture. Mining this distinctive germplasm is therefore essential for identifying novel genetic determinants underlying complex traits like FLM. In this study, a genome-wide association study was conducted on 182 Chinese endemic wheat accessions using 38,490 single-nucleotide polymorphisms. We identified four stable quantitative trait loci (QTL) associated with FLM traits, three of which for flag leaf width (QFLW.sau.5A, QFLW.sau.5B, and QFLW.sau.5D) were intriguingly located on the homoeologous chromosomes of group 5, suggesting the action of a conserved, multi-subgenome genetic system. None of these QTLs overlapped with previously reported loci, highlighting their novelty and the value of this endemic gene pool. Pleiotropic analysis revealed that these loci also influence plant height and spike architecture. Their breeding value was further confirmed by validation in an independent population. Thirteen high-confidence candidate genes with elevated expression in flag leaf tissue were predicted, many involved in leaf development, photosynthesis, and stress responses. Collectively, by mining the unique genetic diversity of Chinese endemic wheat, we have uncovered a novel, homoeologous QTL system and candidate genes for FLM. These findings provide both a conceptual advance in understanding the polyploid genetic architecture of this key trait and valuable functional targets/molecular markers for improving photosynthetic efficiency and yield potential in wheat breeding.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"19 2","pages":"e70245"},"PeriodicalIF":4.3,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13122275/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147786654","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic control of wheat flour end-use quality and rheology by genome-wide association studies.","authors":"Juan Menor de Gaspar, Richard D Cuthbert, Ruan Yuefeng, Ron Knox, BinXiao Fu, Kun Wang, Jatinder S Sangah, Samia Berraies, Brad Meyer, Firdissa E Bokore, Julio Isidro Y Sánchez","doi":"10.1002/tpg2.70236","DOIUrl":"10.1002/tpg2.70236","url":null,"abstract":"<p><p>Improving end-use quality in bread wheat (Triticum aestivum) requires dissecting the genetic basis of complex processing traits and deploying robust prediction pipelines in breeding. We performed genome-wide association studies (GWASs) using 1767 high-quality single-nucleotide polymorphisms generated by genotyping-by-sequencing in a diverse Canada Western Red Spring panel phenotyped near Swift Current, SK, from 2009 to 2019 for grain protein content, milling yield, mixing energy, water absorption, and dough extensibility. The analysis detected significant marker-trait associations on 13 chromosomes, recovering signals at Rht-B1 and Glu-1 and revealing multiple additional signals that may represent previously unreported loci in this germplasm and environmental context, consistent with polygenic control. We then evaluated genomic selection using GBLUP (Genomic Best Linear Unbiased Predictor) and BayesB with and without including significant GWAS hits as fixed effects; gains in predictive accuracy were generally negligible, although water absorption showed modest improvement, compatible with fewer, larger effect loci. Functional annotation of genes near associated variants implicated stress responses, protein metabolism, and grain filling. Together, these results refine the genetic architecture of Canadian wheat quality and support integrating GWAS-informed biology with genome-wide prediction to accelerate quality-by-design breeding.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"19 2","pages":"e70236"},"PeriodicalIF":4.3,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13087497/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147700397","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}