Plant Genome最新文献

{"title":"Genome-wide association study identifies genomic regions under selection for domestication and agronomic traits in intermediate wheatgrass.","authors":"Hannah Stoll, Prabin Bajgain, James A Anderson","doi":"10.1002/tpg2.70258","DOIUrl":"10.1002/tpg2.70258","url":null,"abstract":"<p><p>Intermediate wheatgrass (IWG) (Thinopyrum intermedium, Kernza) is a perennial forage grass undergoing neo-domestication as a grain crop. IWG provides numerous ecosystem services and has the potential to benefit rural communities as an alternative crop option with high market value. However, IWG has only been under development as a perennial grain crop for the past few decades and at the University of Minnesota (UMN) since 2011. Improvements in grain-related traits, market development, and agronomic management are needed for the long-term viability of IWG as a Midwestern grain crop. In this study, 225 parent genets (genetically unique individuals) from UMN IWG breeding Cycles 2, 3, 4, and 5 were cloned, planted, and evaluated for 2 years at two locations. Plants were genotyped using genotyping-by-sequencing to get 12,072 single nucleotide polymorphisms and phenotyped for key domestication and agronomic traits. A genome-wide association study (GWAS) identified 36 quantitative trait loci (QTLs) for shattering, seed size, and yield traits, which individually explained an average of 13% of the phenotypic variation. Several QTLs mapped to the same homoeologous chromosomes or regions as previously identified domestication and agronomic loci in IWG and other cereal species. Changes in allele frequencies for significant QTL across breeding cycles were examined, which identified 12 alleles under selection. Several favorable alleles remain at minor frequencies, indicating substantial potential for continued genetic improvement. Integration of GWAS hits as fixed effects within genomic selection models could enable recurrent selection schemes that strategically increase favorable allele frequencies and stack positive traits for long-term gain.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"19 2","pages":"e70258"},"PeriodicalIF":4.3,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13238349/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148165397","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":"Phenotypic and genetic resistance to Septoria blotch disease in European wheat varieties.","authors":"Conor Copeland, Julio Isidro Y Sánchez, Humberto Fanelli, Fiona M Doohan","doi":"10.1002/tpg2.70237","DOIUrl":"10.1002/tpg2.70237","url":null,"abstract":"<p><p>Zymoseptoria tritici, the causal agent of Septoria tritici blotch (STB), poses a critical threat to wheat (Triticum aestivum L.) production in temperate Europe, underscoring the need for durable genetic resistance. Here, we screened 151 winter wheat varieties at the seedling stage using a mixed inoculum of five virulent isolates. Disease severity was quantified at 14, 21, and 28 days post-inoculation to calculate the area under the disease progress curve. We observed broad phenotypic variation, with higher susceptibility in Southern European germplasm. A genome-wide association study identified three significantly resistant loci: IWB5774 on chromosome 2D, and IWB72742 and IWB11406 on chromosome 1B. Functional annotation mapped these markers to high-priority candidate genes, including a TaBx3D-like protein, the endomembrane trafficking regulator WDR91, and NAP1, a nucleosome assembly factor involved in stress signaling. These findings provide robust molecular markers for breeding and nominate specific targets for functional validation of STB resistance mechanisms.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"19 2","pages":"e70237"},"PeriodicalIF":4.3,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13034100/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147576052","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":"Development and characterization of near-isogenic lines for quantitative trait locus qDT.3B.1 underlying drought tolerance in wheat.","authors":"Joanne D Caguiat, Md Sultan Mia, Hui Liu, Guijun Yan, Kadambot H M Siddique","doi":"10.1002/tpg2.70186","DOIUrl":"10.1002/tpg2.70186","url":null,"abstract":"<p><p>Drought is a critical challenge to wheat (Triticum aestivum L.) productivity. The quantitative complexity of drought tolerance makes breeding for this trait difficult. Developing near-isogenic lines (NILs) targeting quantitative trait locus (QTL) for 1000-grain weight (TGW) under drought stress can effectively identify key mechanisms and genes. Using the heterogeneous inbred family method and a fast-generation cycling system, we developed wheat NILs targeting TGW QTL on chromosome 3B and characterized them under drought and well-watered conditions. Genotyping the NILs using 90K single nucleotide polymorphism (SNP) array, we narrowed down the targeted QTL region and identified four SNP markers near the target QTL linked with six candidate genes. These candidate genes encode beta-glucuronosyltransferase, ABC transporter, transmembrane protein, F-box protein, cytochrome P450, and alanine-tRNA ligase associated with functions related to responses under drought stress. In silico expression analysis revealed that all these candidate genes were highly expressed in root and grain tissues under drought stress and involved in pathways such as ubiquitin-mediated proteolysis, metabolic pathways and biosynthesis of various N-glycan, steroids, and secondary metabolites emphasizing its potential role affecting grain weight under drought stress. This study offers insights into markers and genes controlling TGW under drought and has potential for advancing the development of high-yielding resilient wheat cultivars.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"19 2","pages":"e70186"},"PeriodicalIF":4.3,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13100941/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147786686","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":"Pan-NLRome analysis uncovers genetic diversity and evolutionary dynamics among rice, maize and sorghum.","authors":"Yanbo Wang, Tashi Dorjee, Yinzi Wang, Di Peng, Lang Chen, Chuanzheng Wei, Shichao Sun, Mingyu Duan, Hui Li, Adrian Hathorn, Emma Mace, David Jordan, Xun Wu, Xiaocui Chen, Yongfu Tao","doi":"10.1002/tpg2.70257","DOIUrl":"10.1002/tpg2.70257","url":null,"abstract":"<p><p>Nucleotide-binding leucine-rich repeat (NLR) genes constitute one of the largest families of plant immune receptors and are central to crop disease resistance. Rice (Oryza sativa L.), maize (Zea mays L.), and sorghum (Sorghum bicolor (L.) Moench) are major crops underpinning global food security, and enhancing their immunity is critical for yield stability. Here, we conducted a comprehensive analysis of NLR repertoires across 75 genomes from these three grass crops, identifying 24,944 genes that exhibit extensive intra- and interspecific variation. The crops share broadly comparable domain architectures of NLR genes, despite their differences in gene number and genomic clustering pattern. We detected 68 integrated domains, revealing high diversity and pronounced lineage specificity. The pan-NLR profiles of the three crops were generally similar, with strong lineage-restricted expansion of NLR gene families. Cross-species comparisons revealed distinct proportions of common gene and lineage-specific genes between the crops, suggesting divergent evolutionary trajectories. Widespread presence/absence variation of NLR genes was identified within each crop, with an enrichment in clustered loci. NLRs, especially clustered ones, were significantly enriched in disease-resistance quantitative trait locus (QTL) hotspots, supporting their critical role in crop disease resistance. Notably, conserved Rp1-D clusters co-localized with resistance QTLs in the three crops, underscoring functional conservation and the translational potential of cross-species NLR studies. Collectively, these findings provide new insights into the genetic diversity and evolutionary dynamics of NLRs in three major grass crops and provide a valuable genomic resource for enhancing crop disease resistance.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"19 2","pages":"e70257"},"PeriodicalIF":4.3,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13492628/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148007200","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":"The SD1 locus affects primary seed dormancy in winter malting barley.","authors":"Karl H Kunze, Travis E Rooney, Daniel Sweeney, Mark E Sorrells","doi":"10.1002/tpg2.70234","DOIUrl":"10.1002/tpg2.70234","url":null,"abstract":"<p><p>Preharvest sprouting (PHS) resistance and seed dormancy are key targets for malting barley (Hordeum vulgare L.) in environments with a high probability of rain events at harvest. Characterization has been limited in winter malting barley compared to spring malting barley in the United States. We used a modified half-sibling winter malting barley breeding population to map PHS at maturity and germination traits during after-ripening to identify marker associations with dormancy and rate of dormancy loss. Seed dormancy locus 1 (SD1) on chromosome 5H has been identified as an H. vulgare L. alanine aminotransferase (HvAlaAT) gene. The SD1 locus was significantly associated with the rate of primary seed dormancy loss in the winter malting barley population, and additional quantitative trait loci (QTLs) for PHS resistance and seed dormancy were identified. Identified markers for HvAlaAT alleles and other QTL for seed dormancy can provide greater precision for selecting lines that have high PHS resistance but short dormancy periods to produce high-quality malt.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"19 2","pages":"e70234"},"PeriodicalIF":4.3,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13047305/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147610435","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":"Correction to \"Genome-wide analysis of theAP2/ERF gene family in Rheum officinale Baill.: Evolution and expression profiling during plant development, abiotic stresses, and exogenous hormone responses\".","authors":"","doi":"10.1002/tpg2.70260","DOIUrl":"10.1002/tpg2.70260","url":null,"abstract":"","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"19 2","pages":"e70260"},"PeriodicalIF":4.3,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13492573/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148057733","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 and genomic prediction of anthracnose (Colletotrichum dematium) resistance in spinach.","authors":"Raja Sekhar Srungarapu, Ainong Shi, Carlos A Avila","doi":"10.1002/tpg2.70254","DOIUrl":"10.1002/tpg2.70254","url":null,"abstract":"<p><p>Anthracnose, caused by Colletotrichum dematium, has emerged as a major foliar disease that threatens spinach (Spinacia oleracea L.) production. In this study, a diverse panel of 266 accessions was evaluated under field conditions to dissect the genetic architecture of anthracnose resistance. Substantial phenotypic variation was observed, with disease severity indices (DSIs) ranging from 1 (highly resistant) to 10 (highly susceptible). A total of 20 accessions showed moderate to high resistance (DSI ≤ 4), representing valuable resistance sources. A genome-wide association study (GWAS) identified 20 significant single-nucleotide polymorphisms (SNPs). The most consistent marker (SOVchr3_19667279) explained up to 66.8% of phenotypic variance, and several associated SNPs were located within or near putative defense-related genes. Genomic prediction (GP) using multiple models demonstrated that predictive accuracy increased when a set with more SNPs was used. The genomic best linear unbiased prediction model achieved the highest accuracy (r = 0.92), while the Bayesian ridge regression model attained the best predictive accuracy (r = 0.51) when using 20 GWAS-derived SNPs, highlighting the value of integrating association mapping with prediction approaches. Cross-population prediction performed well (r = 0.58-0.71), whereas across-population prediction showed reduced accuracy (r = 0.10-0.14), indicating the influence of genetic background on model transferability. This integrative genomic study provides novel insights into the genetic basis of anthracnose resistance in spinach and demonstrates the potential of GWAS and GP in accelerating resistance breeding.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"19 2","pages":"e70254"},"PeriodicalIF":4.3,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13492587/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147989812","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":"Traversing the effects of ploidy changes in different Eragrostis curvula genotypes through high-throughput RNA sequencing.","authors":"D F Santoro, J Carballo, M C Pasten, C A Gallo, E Albertini, V Echenique","doi":"10.1002/tpg2.70227","DOIUrl":"10.1002/tpg2.70227","url":null,"abstract":"<p><p>Polyploidization has played a key role in plant genome evolution. Eragrostis curvula (Schrad.) Ness, a perennial forage grass species of the Poaceae family, is an excellent model for investigating genome duplication due to its natural variation in ploidy levels. To explore the transcriptomic consequences of polyploidy, we performed high-throughput RNA-Seq on leaf tissue from 10 E. curvula genotypes ranging from diploid to octoploid. Differential expression analyses revealed that the number of differentially expressed genes increased with increasing ploidy, suggesting a rewiring of the gene regulatory network. Several putative genes associated with stress tolerance and epigenetic regulation were modulated at higher ploidy levels. Forage digestibility and saccharification efficiency were likely altered at higher ploidy levels, mainly due to the upregulation of putative genes involved in lignin biosynthesis, cell wall remodeling, and polysaccharide metabolism. Our results may reveal a fine-tuning regulation favoring stress tolerance over forage digestibility. The analysis of the core set of 433 Ploidy_vs_2x DEGs, consistently expressed in a polyploidy-sensitive manner, revealed upregulation of genes involved in the ubiquitination pathway, stress response, cell wall remodeling, hormonal regulation, and terpenoid biosynthesis. Ploidy-dependent transcriptional responses were also observed in the patterns of transcription factor families, underlining a different reprogramming of the transcriptional network at each ploidy level. An integrated network-based approach combining WGCNA and SWIM (SWItchMiner) identified a predicted master regulator target gene putatively associated with increased forage digestibility. Our findings provide valuable insights into the molecular mechanisms underlying polyploidization in E. curvula, with implications for breeding strategies to balance stress tolerance and biomass digestibility.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"19 2","pages":"e70227"},"PeriodicalIF":4.3,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13032165/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147533795","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 analysis of the AP2/ERF gene family in Rheum officinale Baill.: Evolution and expression profiling during plant development, abiotic stresses, and exogenous hormone responses.","authors":"Jing Tang, Gao-Chang Cui, Heng Pan, Hui Lu, Yi-Min Li, Feng Yan, Jing Gao, Liang Peng, Xiao-Chen Hu, Gang Zhang","doi":"10.1002/tpg2.70248","DOIUrl":"10.1002/tpg2.70248","url":null,"abstract":"<p><p>The APETALA2/ethylene-responsive factor (AP2/ERF) superfamily plays a central role in plant metabolism, stress responses, and hormone signaling. Rheum officinale Baill. is an important traditional medicinal plant whose roots and rhizomes are rich in anthraquinones and other secondary metabolites. However, the regulatory mechanisms underlying its development and secondary metabolism remain unclear, and systematic analyses of its AP2/ERF family are lacking. This study aimed to characterize the genomic features, expression patterns, and potential functions of the AP2/ERF family in R. officinale. A total of 167 RoAP2/ERF genes were identified, unevenly distributed across 11 chromosomes. Gene family expansion was mainly driven by segmental and tandem duplications, with extensive collinearity observed between R. officinale and related species. Phylogenetic, conserved domain, gene structure, and motif analyses classified these genes into five subfamilies (ERF, dehydration reaction element binding factor; AP2, related to abscisic acid insensitive 3/viviparous 1; and Soloist), with similar sequence characteristics within each subfamily. RNA-seq analysis revealed tissue-specific expression patterns, with Cluster 5 genes preferentially expressed in roots and rhizomes. RT-qPCR of 18 representative genes confirmed their involvement in various signaling pathways. RoERF065 and RoERF079 were exclusively nuclear-localized and strongly responsive to stress and hormone treatments. Functional assays indicated that RoERF079 acts as a C-terminal-dependent transcriptional activator, whereas RoERF065 may function as a repressor due to two EAR motifs. These genes may regulate root and rhizome development and secondary metabolism in R. officinale. This study provides a basis for elucidating the molecular mechanisms of organ development and bioactive compound biosynthesis and identifies candidate genes for molecular breeding.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"19 2","pages":"e70248"},"PeriodicalIF":4.3,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13158899/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147870158","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":"Highly heterozygous Citrus changshan-huyou Y. B. Chang originated from ancient hybridization between mandarin and pummelo and displayed distinct tissue-specific allelic imbalance.","authors":"Zhanghui Zeng, Yingjie Luo, Haifei Hu, Lan Lan, Baojin Guo, Ping Zhou, Cong Tan, Xiaoping Huang, Tuo Qi, Zhehao Chen, Zhiming Yu, Lilin Wang, Taihe Xiang, Chengdao Li, Yong Jia","doi":"10.1002/tpg2.70232","DOIUrl":"10.1002/tpg2.70232","url":null,"abstract":"<p><p>The genus Citrus is characterized by a reticulate evolutionary history with frequent hybridization, making it an intriguing subject for genome evolution investigation. Citrus changshan-huyou Y. B. Chang (Huyou) is a unique landrace first discovered in Zhejiang Province, China, with premium fruit quality. The evolutionary origin of Huyou has puzzled local botanists and growers. Here, we sequenced a 120-year-old \"ancestral tree\" of Huyou using PacBio long read and Hi-C sequencing and assembled two high-quality, haplotype-resolved genomes, HY1 and HY2. Huyou displayed a genome heterozygosity level at 3.07%, among the highest in published citrus genomes. Using a k-mer-based tracing approach, we explicitly resolved that HY1 genome contained 87.8% mandarin, 7.3% pummelo, and 0.2% citron origin, whereas HY2 had 85.0% pummelo, 2.9% mandarin, and 0.3% citron, implying a hybridization event between mandarin and pummelo. Phylogeny dating showed that HY1 (2.0 Mya) and HY2 (2.18 Mya) had diverged earlier than the split of Citrus clementina and Citrus reticulata and the split of Citrus grandis and Citrus maxima, respectively. We observed clear chromosomal recombination on chr8 and chr9 in HY1, which may have occurred after the ancestral hybridization. Further transcriptome analyses in six tissues revealed a strong allelic dominance of HY2 over HY1 in root tissue and moderately in stem, leaf, flower, and fruit. Kyoto encyclopedia of genes and genomes (KEGG) enrichment analyses revealed that genes related to antioxidant biosynthesis and lipid metabolism were most significantly affected by allelic imbalance. This pioneering report of allelic imbalance in citrus species support Huyou as an interesting model to investigate genome evolution following distant hybridization.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"19 2","pages":"e70232"},"PeriodicalIF":4.3,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13028926/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147533777","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}