Plant Genome最新文献

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Gene mapping and candidate gene analysis of a sorghum sheathed panicle-I mutant.
IF 3.9 2区 生物学
Plant Genome Pub Date : 2025-03-01 DOI: 10.1002/tpg2.70007
Jianling Ao, Ruoruo Wang, Wenzeng Li, Yanqing Ding, Jianxia Xu, Ning Cao, Xu Gao, Bin Cheng, Degang Zhao, Liyi Zhang
{"title":"Gene mapping and candidate gene analysis of a sorghum sheathed panicle-I mutant.","authors":"Jianling Ao, Ruoruo Wang, Wenzeng Li, Yanqing Ding, Jianxia Xu, Ning Cao, Xu Gao, Bin Cheng, Degang Zhao, Liyi Zhang","doi":"10.1002/tpg2.70007","DOIUrl":"10.1002/tpg2.70007","url":null,"abstract":"<p><p>Panicle exsertion is essential for crop yield and quality, and understanding its molecular mechanisms is crucial for optimizing plant architecture. In this study, the sheathed panicle-I (shp-I) mutant was identified from the ethyl methane sulfonate mutant population of the sorghum [Sorghum bicolor (L.) Moench] variety Hongyingzi (HYZ). While phenotypically similar to the wild type during the seedling stage, shp-I exhibits a significantly shorter peduncle internode at the heading stage. Cytomorphological analysis revealed reduced parenchyma cell size within the mutant's peduncle internode. Phytohormonal profiling showed lower levels of indole-3-acetic acid and higher concentrations of brassinosteroid in the mutant compared to the wild type at the peduncle internode. Genetic analysis confirmed that the mutant phenotype was caused by a recessive single-gene mutation. Through bulked segregant analysis sequencing (BSA-seq) genetic mapping, the causative locus for the mutant phenotype was localized to a 59.65-59.92 Mb interval on chromosome 10, which contains 28 putative genes. Additionally, the gene SbiHYZ.10G230700, which encodes a BTB/POZ and MATH (BPM) domain protein, was identified as a candidate gene. Further analysis revealed that the non-synonymous mutations in the candidate gene were located within the MATH domain, affecting the 3D structure of the protein. In summary, this study provides a new genetic material and candidate genes for future research into the molecular regulation of sorghum peduncle length.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"18 1","pages":"e70007"},"PeriodicalIF":3.9,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11876006/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143544198","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}
引用次数: 0
Phytocytokine genes newly discovered in Malus domestica and their regulation in response to Erwinia amylovora and acibenzolar-S-methyl. 家苹果植物细胞因子基因的新发现及其对淀粉弧菌和酸性苯并- s -甲基的调控。
IF 3.9 2区 生物学
Plant Genome Pub Date : 2025-03-01 Epub Date: 2024-12-08 DOI: 10.1002/tpg2.20540
Marie-Charlotte Guillou, Matthieu Gaucher, Emilie Vergne, Jean-Pierre Renou, Marie-Noëlle Brisset, Sébastien Aubourg
{"title":"Phytocytokine genes newly discovered in Malus domestica and their regulation in response to Erwinia amylovora and acibenzolar-S-methyl.","authors":"Marie-Charlotte Guillou, Matthieu Gaucher, Emilie Vergne, Jean-Pierre Renou, Marie-Noëlle Brisset, Sébastien Aubourg","doi":"10.1002/tpg2.20540","DOIUrl":"10.1002/tpg2.20540","url":null,"abstract":"<p><p>Phytocytokines belong to a category of small secreted peptides with signaling functions that play pivotal roles in diverse plant physiological processes. However, due to low levels of sequence conservation across plant species and poorly understood biological functions, the accurate detection and annotation of corresponding genes is challenging. The availability of a high-quality apple (Malus domestica) genome has enabled the exploration of five phytocytokine gene families, selected on the basis of their altered expression profiles in response to biotic stresses. These include phytosulfokine, inflorescence deficient in abscission/-like, pathogen-associated molecular pattern induced secreted peptide, plant peptide containing sulfated tyrosine, and C-terminally encoded peptide. The genes encoding the precursors of these five families of signaling peptides were identified using a customized bioinformatics protocol combining genome mining, homology searches, and peptide motif detection. Transcriptomic analyses showed that these peptides were deregulated in response to Erwinia amylovora, the causal agent of fire blight in pome fruit trees, and in response to a chemical elicitor (acibenzolar-S-methyl). Finally, gene family evolution and the orthology relationships with Arabidopsis thaliana homologs were investigated.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20540"},"PeriodicalIF":3.9,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11726410/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142795947","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}
引用次数: 0
Identification of robust yield quantitative trait loci derived from cultivated emmer for durum wheat improvement. 栽培二粒小麦高产数量性状位点的鉴定及改良。
IF 3.9 2区 生物学
Plant Genome Pub Date : 2025-03-01 Epub Date: 2023-10-24 DOI: 10.1002/tpg2.20398
Amanda R Peters Haugrud, Jyoti Saini Sharma, Qijun Zhang, Andrew J Green, Steven S Xu, Justin D Faris
{"title":"Identification of robust yield quantitative trait loci derived from cultivated emmer for durum wheat improvement.","authors":"Amanda R Peters Haugrud, Jyoti Saini Sharma, Qijun Zhang, Andrew J Green, Steven S Xu, Justin D Faris","doi":"10.1002/tpg2.20398","DOIUrl":"10.1002/tpg2.20398","url":null,"abstract":"<p><p>Durum wheat (Triticum turgidum ssp. durum L.) is an important world food crop used to make pasta products. Compared to bread wheat (Triticum aestivum L.), fewer studies have been conducted to identify genetic loci governing yield-component traits in durum wheat. A potential source of diversity for durum is its immediate progenitor, cultivated emmer (T. turgidum ssp. dicoccum). We evaluated two biparental populations of recombinant inbred lines (RILs) derived from crosses between the durum lines Ben and Rusty and the cultivated emmer wheat accessions PI 41025 and PI 193883, referred to as the Ben × PI 41025 (BP025) and Rusty × PI 193883 (RP883) RIL populations, respectively. Both populations were evaluated under field conditions in three seasons with an aim to identify quantitative trait loci (QTLs) associated with yield components and seed morphology that were expressed in multiple environments. A total of 44 and 34 multi-environment QTLs were identified in the BP025 and RP883 populations, respectively. As expected, genetic loci known to govern domestication and development were associated with some of the QTLs, but novel QTLs derived from the cultivated emmer parents and associated with yield components including spikelet number, grain weight, and grain size were identified. These QTLs offer new target loci for durum wheat improvement, and toward that goal, we identified five RILs with increased grain weight and size compared to the durum parents. These materials along with the knowledge of stable QTLs and associated markers can help to expedite the development of superior durum varieties.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20398"},"PeriodicalIF":3.9,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11726405/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50159101","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}
引用次数: 0
Chromosome-level genome assembly of Iodes seguinii and its metabonomic implications for rheumatoid arthritis treatment. Iodes seguinii 染色体级基因组组装及其对类风湿性关节炎治疗的代谢影响。
IF 3.9 2区 生物学
Plant Genome Pub Date : 2025-03-01 Epub Date: 2024-11-27 DOI: 10.1002/tpg2.20534
Xun Gong, Hantao Zhang, Yinluo Guo, Shaoshuai Yu, Min Tang
{"title":"Chromosome-level genome assembly of Iodes seguinii and its metabonomic implications for rheumatoid arthritis treatment.","authors":"Xun Gong, Hantao Zhang, Yinluo Guo, Shaoshuai Yu, Min Tang","doi":"10.1002/tpg2.20534","DOIUrl":"10.1002/tpg2.20534","url":null,"abstract":"<p><p>Iodes seguinii is a woody vine known for its potential therapeutic applications in treating rheumatoid arthritis (RA) due to its rich bioactive components. Here, we achieved the first chromosome-level assembly of the nuclear genome of I. seguinii using PacBio HiFi and chromatin conformation capture (Hi-C) sequencing data. The initial assembly with PacBio data produced contigs with an N50 length of 9.71 Mb, and Hi-C data anchored these contigs into 13 chromosomes, achieving a total length of 273.58 Mb, closely matching the estimated genome size. Quality assessments, including BUSCO, long terminal repeat assembly index, transcriptome mapping rates, and sequencing coverage, confirmed the high quality, completeness, and continuity of the assembly, identifying 115.28 Mb of repetitive sequences, 1062 RNA genes, and 25,270 protein-coding genes. Additionally, we assembled and annotated the 150,599 bp chloroplast genome using Illumina sequencing data, containing 121 genes including key DNA barcodes, with maturase K (matK) proving effective for species identification. Phylogenetic analysis positioned I. seguinii at the base of the Lamiales clade, identifying significant gene family expansions and contractions, particularly related to secondary metabolite synthesis and DNA damage repair. Metabolite analysis identified 84 active components in I. seguinii, including the discovery of luteolin, with 119 targets predicted for RA treatment, including core targets like AKT1, toll-like receptor 4 (TLR4), epidermal growth factor receptor (EGFR), tumor necrosis factor (TNF), TP53, NFKB1, janus kinase 2 (JAK2), BCL2, mitogen-activated protein kinase 1 (MAPK1), and spleen-associated tyrosine kinase (SYK). Key active components such as flavonoids and polyphenols with anti-inflammatory activities were highlighted. The discovery of luteolin, in particular, underscores its potential therapeutic role. These findings provide a valuable genomic resource and a scientific basis for the development and application of I. seguinii, addressing the genomic gap in the genus Iodes and the order Icacinales and underscoring the need for further research in genomics, transcriptomics, and metabolomics to fully explore its potential.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20534"},"PeriodicalIF":3.9,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11729983/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142740850","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}
引用次数: 0
Future of durum wheat research and breeding: Insights from early career researchers. 硬粒小麦研究和育种的未来:早期职业研究人员的见解。
IF 3.9 2区 生物学
Plant Genome Pub Date : 2025-03-01 Epub Date: 2024-05-17 DOI: 10.1002/tpg2.20453
Amanda R Peters Haugrud, Ana Laura Achilli, Raquel Martínez-Peña, Valentyna Klymiuk
{"title":"Future of durum wheat research and breeding: Insights from early career researchers.","authors":"Amanda R Peters Haugrud, Ana Laura Achilli, Raquel Martínez-Peña, Valentyna Klymiuk","doi":"10.1002/tpg2.20453","DOIUrl":"10.1002/tpg2.20453","url":null,"abstract":"<p><p>Durum wheat (Triticum turgidum ssp. durum) is globally cultivated for pasta, couscous, and bulgur production. With the changing climate and growing world population, the need to significantly increase durum production to meet the anticipated demand is paramount. This review summarizes recent advancements in durum research, encompassing the exploitation of existing and novel genetic diversity, exploration of potential new diversity sources, breeding for climate-resilient varieties, enhancements in production and management practices, and the utilization of modern technologies in breeding and cultivar development. In comparison to bread wheat (T. aestivum), the durum wheat community and production area are considerably smaller, often comprising many small-family farmers, notably in African and Asian countries. Public breeding programs such as the International Maize and Wheat Improvement Center (CIMMYT) and the International Center for Agricultural Research in the Dry Areas (ICARDA) play a pivotal role in providing new and adapted cultivars for these small-scale growers. We spotlight the contributions of these and others in this review. Additionally, we offer our recommendations on key areas for the durum research community to explore in addressing the challenges posed by climate change while striving to enhance durum production and sustainability. As part of the Wheat Initiative, the Expert Working Group on Durum Wheat Genomics and Breeding recognizes the significance of collaborative efforts in advancing toward a shared objective. We hope the insights presented in this review stimulate future research and deliberations on the trajectory for durum wheat genomics and breeding.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20453"},"PeriodicalIF":3.9,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11733671/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140960444","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}
引用次数: 0
Enhancing prediction accuracy of grain yield in wheat lines adapted to the southeastern United States through multivariate and multi-environment genomic prediction models incorporating spectral and thermal information. 通过结合光谱和热信息的多变量和多环境基因组预测模型,提高适应美国东南部地区的小麦品系的谷物产量预测准确性。
IF 3.9 2区 生物学
Plant Genome Pub Date : 2025-03-01 Epub Date: 2024-11-19 DOI: 10.1002/tpg2.20532
Jordan McBreen, Md Ali Babar, Diego Jarquin, Naeem Khan, Steve Harrison, Noah DeWitt, Mohamed Mergoum, Ben Lopez, Richard Boyles, Jeanette Lyerly, J Paul Murphy, Ehsan Shakiba, Russel Sutton, Amir Ibrahim, Kimberly Howell, Jared H Smith, Gina Brown-Guedira, Vijay Tiwari, Nicholas Santantonio, David A Van Sanford
{"title":"Enhancing prediction accuracy of grain yield in wheat lines adapted to the southeastern United States through multivariate and multi-environment genomic prediction models incorporating spectral and thermal information.","authors":"Jordan McBreen, Md Ali Babar, Diego Jarquin, Naeem Khan, Steve Harrison, Noah DeWitt, Mohamed Mergoum, Ben Lopez, Richard Boyles, Jeanette Lyerly, J Paul Murphy, Ehsan Shakiba, Russel Sutton, Amir Ibrahim, Kimberly Howell, Jared H Smith, Gina Brown-Guedira, Vijay Tiwari, Nicholas Santantonio, David A Van Sanford","doi":"10.1002/tpg2.20532","DOIUrl":"10.1002/tpg2.20532","url":null,"abstract":"<p><p>Enhancing predictive modeling accuracy in wheat (Triticum aestivum) breeding through the integration of high-throughput phenotyping (HTP) data with genomic information is crucial for maximizing genetic gain. In this study, spanning four locations in the southeastern United States over 3 years, models to predict grain yield (GY) were investigated through different cross-validation approaches. The results demonstrate the superiority of multivariate comprehensive models that incorporate both genomic and HTP data, particularly in accurately predicting GY across diverse locations and years. These HTP-incorporating models achieve prediction accuracies ranging from 0.59 to 0.68, compared to 0.40-0.54 for genomic-only models when tested under different prediction scenarios both across years and locations. The comprehensive models exhibit superior generalization to new environments and achieve the highest accuracy when trained on diverse datasets. Predictive accuracy improves as models incorporate data from multiple years, highlighting the importance of considering temporal dynamics in modeling approaches. The study reveals that multivariate prediction outperformed genomic prediction methods in predicting lines across years and locations. The percentage of top 25% lines selected based on multivariate prediction was higher compared to genomic-only models, indicated by higher specificity, which is the proportion of correctly identified top-yielding lines that matched the observed top 25% performance across different sites and years. Additionally, the study addresses the prediction of untested locations based on other locations within the same year and in new years at previously tested locations. Findings show the comprehensive models effectively extrapolate to new environments, highlighting their potential for guiding breeding strategies.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20532"},"PeriodicalIF":3.9,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11726420/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142677430","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}
引用次数: 0
Camelina circRNA landscape: Implications for gene regulation and fatty acid metabolism. 荠菜 circRNA 图谱:对基因调控和脂肪酸代谢的影响。
IF 3.9 2区 生物学
Plant Genome Pub Date : 2025-03-01 Epub Date: 2024-12-10 DOI: 10.1002/tpg2.20537
Delecia Utley, Brianne Edwards, Asa Budnick, Erich Grotewold, Heike Sederoff
{"title":"Camelina circRNA landscape: Implications for gene regulation and fatty acid metabolism.","authors":"Delecia Utley, Brianne Edwards, Asa Budnick, Erich Grotewold, Heike Sederoff","doi":"10.1002/tpg2.20537","DOIUrl":"10.1002/tpg2.20537","url":null,"abstract":"<p><p>Circular RNAs (circRNAs) are closed-loop RNAs forming a covalent bond between their 3' and 5' ends, the back splice junction (BSJ), rendering them resistant to exonucleases and thus more stable compared to linear RNAs. Identification of circRNAs and distinction from their cognate linear RNA is only possible by sequencing the BSJ that is unique to the circRNA. CircRNAs are involved in the regulation of their cognate RNAs by increasing transcription rates, RNA stability, and alternative splicing. We have identified circRNAs from C. sativa that are associated with the regulation of germination, light response, and lipid metabolism. We sequenced light-grown and etiolated seedlings after 5 or 7 days post-germination and identified a total of 3447 circRNAs from 2763 genes. Most circRNAs originate from a single homeolog of the three subgenomes from allohexaploid camelina and correlate with higher ratios of alternative splicing of their cognate genes. A network analysis shows the interactions of select miRNA:circRNA:mRNAs for regulation of transcript stabilities where circRNA can act as a competing endogenous RNA. Several key lipid metabolism genes can generate circRNA, and we confirmed the presence of KASII circRNA as a true circRNA. CircRNA in camelina can be a novel target for breeding and engineering efforts.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20537"},"PeriodicalIF":3.9,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11726430/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142830617","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}
引用次数: 0
Genome-wide identification of WOX family members in rose and functional analysis of RcWUS1 in embryogenic transformation.
IF 3.9 2区 生物学
Plant Genome Pub Date : 2025-03-01 DOI: 10.1002/tpg2.70012
Xue Bai, Qi Fu, Weikun Jing, Hao Zhang, Hongying Jian, Xianqin Qiu, Hongjie Li, Qigang Wang, Shunting Yang, Yiping Zhang, Huichun Wang, Lihua Wang, Kaixue Tang, Ying Bao, Huijun Yan
{"title":"Genome-wide identification of WOX family members in rose and functional analysis of RcWUS1 in embryogenic transformation.","authors":"Xue Bai, Qi Fu, Weikun Jing, Hao Zhang, Hongying Jian, Xianqin Qiu, Hongjie Li, Qigang Wang, Shunting Yang, Yiping Zhang, Huichun Wang, Lihua Wang, Kaixue Tang, Ying Bao, Huijun Yan","doi":"10.1002/tpg2.70012","DOIUrl":"10.1002/tpg2.70012","url":null,"abstract":"<p><p>WUSCHEL-related homeobox (WOX) is a class of plant-specific transcription factors and plays vital roles in plant development and evolution. Here, we analyzed WOX family genes of three Rosa species and explored their potential functions in Rosa. A total of 351 WOX genes were identified from Rosa chinensis 'Old Blush' (208), Rosa wichuraiana 'Basye's Thornless' (21) and Rosa rugosa (122). The WOX genes were found to significantly expand in Rosa compared to Arabidopsis. Phylogenetic analysis showed that Rosa WOXs genes were classified into an ancient clade, an intermediate clade, and a WUS clade. Collinearity analysis suggested that gene duplication and purifying selection might be important driving forces in the evolution of WOXs. Expression patterns of WOXs found that higher levels of RcWUS1 expression were detected at the shoot apex somatic embryos. Furthermore, we found that RcWUS1 was a transcriptional repressor located in the nucleus. Overexpression of RcWUS1 enhanced the regeneration efficiency of somatic embryos. In summary, our results indicated the functional potential of RcWUS1 in embryogenic transformation, which can be further utilized to improve the genetic transformation efficiency in rose.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"18 1","pages":"e70012"},"PeriodicalIF":3.9,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11873168/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143537994","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}
引用次数: 0
Using genome-wide associations and host-by-pathogen predictions to identify allelic interactions that control disease resistance.
IF 3.9 2区 生物学
Plant Genome Pub Date : 2025-03-01 DOI: 10.1002/tpg2.70006
Owen Hudson, Jeremy Brawner
{"title":"Using genome-wide associations and host-by-pathogen predictions to identify allelic interactions that control disease resistance.","authors":"Owen Hudson, Jeremy Brawner","doi":"10.1002/tpg2.70006","DOIUrl":"10.1002/tpg2.70006","url":null,"abstract":"<p><p>Characterizing the molecular mechanisms underlying disease symptom expression has been used to improve human health and disease resistance in crops and animal breeds. Quantitative trait loci and genome-wide association studies (GWAS) are widely used to identify genomic regions that are involved in disease progression. This study extends traditional GWAS significance tests of host and pathogen marker main effects by utilizing dual-genome reaction norm models to evaluate the importance of host-single nucleotide polymorphism (SNP) by pathogen-SNP interactions. Disease symptom severity data from Fusarium ear rot (FER) on maize (Zea mays L.) is used to demonstrate the use of both genomes in genomic selection models for breeding and the identification of loci that interact across organisms to impact FER disease development. Dual genome prediction models improved heritability estimates, error variances, and model accuracy while providing predictions for host-by-pathogen interactions that may be used to test the significance of SNP-SNP interactions. Independent GWAS for maize and Fusarium populations identified significantly associated loci and predictions that were used to evaluate the importance of interactions using two different association tests. Predictions from dual genome models were used to evaluate the significance of the SNP-SNP interactions that may be associated with population structure or polygenic effects. As well, association tests incorporating host and pathogen markers in models that also included genomic relationship matrices were used to account for population structure. Subsequent evaluation of protein-protein interactions from candidate genes near the interacting SNPs provides a further in silico evaluation method to expedite the identification of interacting genes.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"18 1","pages":"e70006"},"PeriodicalIF":3.9,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11850958/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143494402","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}
引用次数: 0
Brassica Panache: A multi-species graph pangenome representing presence absence variation across forty-one Brassica genomes. 十字花科:一个多物种图泛基因组,代表了41个十字花科基因组的存在缺失变异。
IF 3.9 2区 生物学
Plant Genome Pub Date : 2025-03-01 Epub Date: 2024-12-08 DOI: 10.1002/tpg2.20535
Tessa R MacNish, Hawlader A Al-Mamun, Philipp E Bayer, Connor McPhan, Cassandria G Tay Fernandez, Shriprabha R Upadhyaya, Shengyi Liu, Jacqueline Batley, Isobel A P Parkin, Andrew G Sharpe, David Edwards
{"title":"Brassica Panache: A multi-species graph pangenome representing presence absence variation across forty-one Brassica genomes.","authors":"Tessa R MacNish, Hawlader A Al-Mamun, Philipp E Bayer, Connor McPhan, Cassandria G Tay Fernandez, Shriprabha R Upadhyaya, Shengyi Liu, Jacqueline Batley, Isobel A P Parkin, Andrew G Sharpe, David Edwards","doi":"10.1002/tpg2.20535","DOIUrl":"10.1002/tpg2.20535","url":null,"abstract":"<p><p>Brassicas are an economically important crop species that provide a source of healthy oil and vegetables. With the rising population and the impact of climate change on agriculture, there is an increasing need to improve agronomically important traits of crops such as Brassica. The genomes of plant species have significant sequence presence absence variation (PAV), which is a source of genetic variation that can be used for crop improvement, and this species variation can be captured through the construction of pangenomes. Graph pangenomes are a recent reference format that represent the genomic variation with a species or population as alternate paths in a sequence graph. Graph pangenomes contain information on alignment, PAV, and annotation. Here we present the first multi-species graph pangenome for Brassica visualized with pangenome analyzer with chromosomal exploration (Panache).</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20535"},"PeriodicalIF":3.9,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11730171/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142795869","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}
引用次数: 0
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