Plant Genome最新文献

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 : 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":"https://doi.org/10.1002/tpg2.20537","url":null,"abstract":"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.","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20537"},"PeriodicalIF":3.9,"publicationDate":"2024-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Mapping resistance to Sclerotinia white mold in two pinto bean recombinant inbred line populations.

IF 3.9 2区生物学

Plant Genome Pub Date : 2024-12-09 DOI: 10.1002/tpg2.20538

Alvaro Soler-Garzón, Fernanda Souza Lopes, Jayanta Roy, Josh Clevenger, Zachary Myers, Walid Korani, Welison Andrade Pereira, Qijian Song, Timothy Porch, Phillip E McClean, Phillip N Miklas

{"title":"Mapping resistance to Sclerotinia white mold in two pinto bean recombinant inbred line populations.","authors":"Alvaro Soler-Garzón, Fernanda Souza Lopes, Jayanta Roy, Josh Clevenger, Zachary Myers, Walid Korani, Welison Andrade Pereira, Qijian Song, Timothy Porch, Phillip E McClean, Phillip N Miklas","doi":"10.1002/tpg2.20538","DOIUrl":"https://doi.org/10.1002/tpg2.20538","url":null,"abstract":"White mold, caused by the fungus Sclerotinia sclerotiorum (Lib.) de Bary, is a devastating disease affecting common bean (Phaseolus vulgaris L.) production worldwide. Breeding for resistance to white mold is challenging due to its quantitative inheritance and intricate genetic mechanisms. This research aimed to validate and characterize physiological resistance in the pinto dry bean market class through greenhouse straw tests under controlled conditions and field assessments under natural environments. Classical quantitative trait locus (QTL) mapping and Khufu de novo QTL-seq were employed to detect and narrow QTL intervals and identify candidate genes associated with white mold resistance in two pinto bean recombinant inbred line populations, PT9-5-6/USPT-WM-12 (P2) and PT12-37/VCP-13 (P3). Eleven QTL, five in P2 and six in P3, conditioning white mold resistance were identified. New QTL were discovered including WM1.4 and WM11.5 in P2, and WM1.5 and WM7.7 in P3. Existing major-effect QTL were validated: WM5.4 (34%-phenotypic variation explained) and WM7.4 (20%) in straw tests, and WM2.2 (15%) and WM3.1 (27%) under field conditions. QTL for avoidance traits such as resistance to lodging and late maturity overlapped WM2.2 in P2 and WM1.5, WM3.1, WM5.4, and WM7.7 in P3. WM5.4 (Pv05: 7.0-38.7 Mb) was associated with a large Phaseolus coccineus L. genome introgression in the resistant parent VCP-13. These findings offer narrowed genomic intervals and putative candidate genes for marker-assisted selection targeting white mold resistance improvement in pinto beans.","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20538"},"PeriodicalIF":3.9,"publicationDate":"2024-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142802886","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","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.

IF 3.9 2区生物学

Plant Genome Pub 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":"https://doi.org/10.1002/tpg2.20540","url":null,"abstract":"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.","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20540"},"PeriodicalIF":3.9,"publicationDate":"2024-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","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.

IF 3.9 2区生物学

Plant Genome Pub 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

引用次数: 0

Optimization of high-throughput marker systems for genomic prediction in alfalfa family bulks.

IF 3.9 2区生物学

Plant Genome Pub Date : 2024-12-05 DOI: 10.1002/tpg2.20526

Pablo Sipowicz, Mario Henrique Murad Leite Andrade, Claudio Carlos Fernandes Filho, Juliana Benevenuto, Patricio Muñoz, L Felipe V Ferrão, Marcio F R Resende, C Messina, Esteban F Rios

{"title":"Optimization of high-throughput marker systems for genomic prediction in alfalfa family bulks.","authors":"Pablo Sipowicz, Mario Henrique Murad Leite Andrade, Claudio Carlos Fernandes Filho, Juliana Benevenuto, Patricio Muñoz, L Felipe V Ferrão, Marcio F R Resende, C Messina, Esteban F Rios","doi":"10.1002/tpg2.20526","DOIUrl":"https://doi.org/10.1002/tpg2.20526","url":null,"abstract":"Alfalfa (Medicago sativa L.) is a perennial forage legume esteemed for its exceptional quality and dry matter yield (DMY); however, alfalfa has historically exhibited low genetic gain for DMY. Advances in genotyping platforms paved the way for a cost-effective application of genomic prediction in alfalfa family bulks. In this context, the optimization of marker density holds potential to reallocate resources within genomic prediction pipelines. This study aimed to (i) test two genotyping platforms for population structure discrimination and predictive ability (PA) of genomic prediction models (G-BLUP) for DMY, and (ii) explore optimal levels of marker density to predict DMY in family bulks. For this, 160 nondormant alfalfa families were phenotyped for DMY across 11 harvests and genotyped via targeted sequencing using Capture-seq with 17K probes and the DArTag 3K panel. Both platforms discriminated similarly against the population structure and resulted in comparable PA for DMY. For genotyping optimization, different levels of marker density were randomly extracted from each platform. In both cases, a plateau was achieved around 500 markers, yielding similar PA as the full set of markers. For phenotyping optimization, models with 500 markers built with data from five harvests resulted in similar PA compared to the full set of 11 harvests and full set of markers. Altogether, genotyping and phenotyping efforts were optimized in terms of number of markers and harvests. Capture-seq and DArTag yielded similar results and have the flexibility to adjust their panels to meet breeders' needs in terms of marker density.","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20526"},"PeriodicalIF":3.9,"publicationDate":"2024-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142787441","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Exon disruptive variants in Populus trichocarpa associated with wood properties exhibit distinct gene expression patterns.

IF 3.9 2区生物学

Plant Genome Pub Date : 2024-12-04 DOI: 10.1002/tpg2.20541

Anthony Piot, Yousry A El-Kassaby, Ilga Porth

{"title":"Exon disruptive variants in Populus trichocarpa associated with wood properties exhibit distinct gene expression patterns.","authors":"Anthony Piot, Yousry A El-Kassaby, Ilga Porth","doi":"10.1002/tpg2.20541","DOIUrl":"https://doi.org/10.1002/tpg2.20541","url":null,"abstract":"Forest trees may harbor naturally occurring exon disruptive variants (DVs) in their gene sequences, which potentially impact important ecological and economic phenotypic traits. However, the abundance and molecular regulation of these variants remain largely unexplored. Here, 24,420 DVs were identified by screening 1014 Populus trichocarpa full genomes. The identified DVs were predominantly heterozygous with allelic frequencies below 5% (only 26% of DVs had frequencies greater than 5%). Using common garden-grown trees, DVs were assessed for gene expression variation in the developing xylem, revealing that their gene expression can be significantly altered, particularly for homozygous DVs (in the range of 27%-38% of cases depending on the studied common garden). DVs were further investigated for their correlations with 13 wood quality traits, revealing that, among the 148 discovered DV associations, 15 correlated with more than one wood property and six genes had more than one DV in their coding sequences associated with wood traits. Approximately one-third of DVs correlated with wood property variation also showed significant gene expression variation, confirming their non-spurious impact. These findings offer potential avenues for targeted introduction of homozygous mutations using tree biotechnology, and while the exact mechanisms by which DVs may directly influence wood formation remain to be unraveled, this study lays the groundwork for further investigation.","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20541"},"PeriodicalIF":3.9,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142780906","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genome-wide association of an organic naked barley diversity panel identified quantitative trait loci for disease resistance. 有机裸麦多样性面板的全基因组关联确定了抗病性的数量性状位点。

IF 3.9 2区生物学

Plant Genome Pub Date : 2024-12-01 Epub Date: 2024-11-14 DOI: 10.1002/tpg2.20530

Karl H Kunze, Brigid Meints, Chris Massman, Lucia Gutiérrez, Patrick M Hayes, Kevin P Smith, Gary C Bergstrom, Mark E Sorrells

{"title":"Genome-wide association of an organic naked barley diversity panel identified quantitative trait loci for disease resistance.","authors":"Karl H Kunze, Brigid Meints, Chris Massman, Lucia Gutiérrez, Patrick M Hayes, Kevin P Smith, Gary C Bergstrom, Mark E Sorrells","doi":"10.1002/tpg2.20530","DOIUrl":"10.1002/tpg2.20530","url":null,"abstract":"Foliar fungal diseases are a major limitation in organic naked barley (Hordeum vulgare L.) production. The lack of conventional fungicides in organic systems increases reliance on genetic resistance. We evaluated the severity of barley stripe rust (Puccinia striiformis f. sp. hordei Westend), leaf rust (Puccina hordei sp. hordei), spot blotch (Cochliobolus sativus, anamorph Bipolaris sorokiniana (S. Ito & Kurib.) Drechsler ex Dastur), and scald (Rhynchosporium commune Zaffarano, McDonald and Linde sp. nov) on a naked barley diversity panel of 350 genotypes grown in 13 environments to identify quantitative trait loci associated with disease resistance. Genome-wide association analyses across and within environments found 10 marker trait associations for barley stripe rust, four marker trait associations for leaf rust, one marker trait association for scald, and five marker trait associations for spot blotch. Structure analysis identified six Ward groups based on genotypic diversity. Resistance to susceptible allele ratios were high for stripe rust and spot blotch, moderate for leaf rust, and low for scald. Combined phenotypic analysis values for each disease overlayed by a principal component analysis found distinct resistance and susceptibility patterns for barley stripe rust and scald. Most significant marker trait associations were previously identified in the literature, providing confirmation and potential new sources of disease resistance for genetic improvement of naked barley germplasm.","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20530"},"PeriodicalIF":3.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11628886/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142631000","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

A graph model for genomic prediction in the context of a linear mixed model framework. 线性混合模型框架下的基因组预测图模型。

IF 3.9 2区生物学

Plant Genome Pub Date : 2024-12-01 Epub Date: 2024-10-07 DOI: 10.1002/tpg2.20522

Osval A Montesinos-López, Gloria Isabel Huerta Prado, José Cricelio Montesinos-López, Abelardo Montesinos-López, José Crossa

引用次数: 0

Genome-wide association study and KASP marker development for starch quality traits in wheat. 小麦淀粉品质性状的全基因组关联研究和 KASP 标记开发。

IF 3.9 2区生物学

Plant Genome Pub Date : 2024-12-01 Epub Date: 2024-09-29 DOI: 10.1002/tpg2.20514

Yousheng Tian, Pengpeng Liu, Xin Zhang, Yichen Liu, Dezhen Kong, Yingbin Nie, Hongjun Xu, Xinnian Han, Wei Sang, Weihua Li

{"title":"Genome-wide association study and KASP marker development for starch quality traits in wheat.","authors":"Yousheng Tian, Pengpeng Liu, Xin Zhang, Yichen Liu, Dezhen Kong, Yingbin Nie, Hongjun Xu, Xinnian Han, Wei Sang, Weihua Li","doi":"10.1002/tpg2.20514","DOIUrl":"10.1002/tpg2.20514","url":null,"abstract":"Starch is the main component of wheat (Triticum aestivum L.) flour, and its quality directly affects the processing quality of the final product. To investigate the genetic basis of starch, this study assessed the starch quality traits of 341 winter wheat varieties/lines grown in Emin and Qitai during the years 2019-2020 and 2020-2021. A genome-wide association study was conducted with the genotype data obtained from wheat 40K breeding chips using the mixed linear model. Wheat starch quality traits exhibited coefficients of variation ranging from 1.43% to 23.66% and broad-sense heritabilities between 0.37 and 0.87. All traits followed an approximately normal distribution, except for T. There were highly significant correlations among starch quality traits, with the strongest correlation observed between final viscosity (FV) and trough viscosity (TV) (r = 0.748), followed by peak viscosity and breakdown (BD) (r = 0.679). Thirty-four single-nucleotide polymorphism markers significantly and stably associated with starch quality traits were identified, clustering in 31 genetic loci. These included one locus for TV, six loci for BD, three loci for FV, two loci for peak time (PT), 12 loci for T, five loci for falling number, and two loci for damaged starch. One PT-related block of 410 kb was identified in the region of 596 Mb on chromosome 5A, where significant phenotypic differences were observed between different haplotypes. One Kompetitive allele-specific PCR (KASP) marker for T was developed on chromosome 7B, and two KASP markers for BD were developed on chromosome 7A. Four candidate genes possibly affecting BD during grain development were identified on chromosome 7A, including TraesCS7A02G225100.1, TraesCS7A02G225900.1, TraesCS7A02G226400.1, and TraesCS7A02G257100.1. The results have significant implications for utilizing marker-assisted selection in breeding to improve wheat starch quality.","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20514"},"PeriodicalIF":3.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11628900/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142330655","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 and mapping of QTLs and their corresponding candidate genes controlling high night-time temperature stress tolerance in wheat (Triticum aestivum L.). 控制小麦（Triticum aestivum L.）耐受夜间高温胁迫的 QTLs 及其相应候选基因的鉴定和绘图。

IF 3.9 2区生物学

Plant Genome Pub Date : 2024-12-01 Epub Date: 2024-09-24 DOI: 10.1002/tpg2.20517

Kaviraj S Kahlon, Kanwardeep S Rawale, Sachin Kumar, Kulvinder S Gill

{"title":"Identification and mapping of QTLs and their corresponding candidate genes controlling high night-time temperature stress tolerance in wheat (Triticum aestivum L.).","authors":"Kaviraj S Kahlon, Kanwardeep S Rawale, Sachin Kumar, Kulvinder S Gill","doi":"10.1002/tpg2.20517","DOIUrl":"10.1002/tpg2.20517","url":null,"abstract":"With every 1°C rise in temperature, yields are predicted to decrease by 5%-6% for both cool and warm season crops, threatening food production, which should double by 2050 to meet the global demand. While high night-time temperature (HNT) stress is expected to increase due to climate change, limited information is available on the genetic control of the trait, especially in wheat (Triticum aestivum L.). To identify genes controlling the HNT trait, we evaluated a doubled haploid (DH) population developed from a cross between an HNT tolerant line KSG1203 and KSG0057, a selection out of a mega variety PBW343 from South East Asia that turned out to be HNT susceptible. The population, along with the parents, were evaluated under 30°C night-time (HNT stress) keeping the daytime temperature to normal 22°C. The same daytime and 16°C night-time temperature were used as a control. The HNT treatment negatively impacted all agronomic traits under evaluation, with a percentage reduction of 0.5%-35% for the tolerant parent, 8%-75% for the susceptible parent, and 8%-50% for the DH population. Performed using sequencing-based genotyping, quantitative trait locus (QTL) mapping identified 19 QTLs on 13 wheat chromosomes explaining 9.72%-28.81% of cumulative phenotypic variance for HNT stress tolerance, along with 13 that were for traits under normal growing conditions. The size of QTL intervals ranged between 0.021 and 97.48 Mb, with the number of genes ranging between 2 and 867. A candidate gene analysis for the smallest six QTL intervals identified eight putative candidates for night-time heat stress tolerance.","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20517"},"PeriodicalIF":3.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11628910/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142330656","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