Plant Genome最新文献

{"title":"AtSubP-2.0: An integrated web server for the annotation of Arabidopsis proteome subcellular localization using deep learning.","authors":"Naveen Duhan, Rakesh Kaundal","doi":"10.1002/tpg2.20536","DOIUrl":"10.1002/tpg2.20536","url":null,"abstract":"<p><p>The organization of subcellular components in a cell is critical for its function and studying cellular processes, protein-protein interactions, identifying potential drug targets, network analysis, and other systems biology mechanisms. Determining protein localization experimentally is time-consuming and expensive. Due to the need for meticulous experimentation, validation, and data analysis, computational methods provide a quick and accurate alternative. Arabidopsis thaliana, a beneficial model organism in plant biology, facilitates experimentation and applies to other plants. Predicting its proteins' subcellular localization can improve our understanding of cellular processes and have applications in crop improvement and biotechnology. We propose AtSubP-2.0, an extension of our previously developed and widely used AtSubP v1.0 tool for annotating the Arabidopsis proteome. For precise protein subcellular localization prediction, AtSubP-2.0 employs a four-phase strategy. The first phase differentiates between single and dual localization with accuracy (97.66% in fivefold training/testing, 98.10% on independent data) and high Matthews correlation coefficient (0.88 training, 0.90 independent). Single localized proteins are classified into 12 locations at the second phase, with accuracy (98.37% in fivefold training/testing, 97.43% on independent data) and Matthews correlation coefficient (0.94 training, 0.91 independent). The third phase categorizes dual location proteins into nine classes with accuracy (99.65% in fivefold training/testing, 98.16% on independent data) and Matthews correlation coefficient (0.92 training, 0.87 independent). We also employed a fourth phase that classifies the membrane type proteins predicted in phase I into single-pass and multi-pass membrane with accuracy (98% in fivefold training/testing, 98.55% on independent data) and a high Matthews correlation coefficient (0.95 training, 0.97 independent). A web-based prediction server has been implemented for community use and is freely available at https://kaabil.net/AtSubP2/, including a standalone version. AtSubP2 will help researchers to better understand organelle-specific functions, cellular processes, and regulatory mechanisms important for plant growth, development, and response to environmental stimuli.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"18 1","pages":"e20536"},"PeriodicalIF":3.9,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11807733/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143383655","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":"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}

{"title":"Genome sequencing of three Polyscias species reveals common features in terpene synthase gene family evolution in these species.","authors":"Mingzhou Bai, Xin Yang, David H Lorence, Kenneth R Wood, Natalie Iwanycki Ahlstrand, Timothy W Flynn, Shancen Zhao, Nina Rønsted, Henrik Toft Simonsen","doi":"10.1002/tpg2.20563","DOIUrl":"10.1002/tpg2.20563","url":null,"abstract":"<p><p>The genus Polyscias, part of the Araliaceae family, is known for its significant ornamental and medicinal value, as well as its rich variety of metabolites. These plants are primarily found in tropical regions, particularly in Southeast Asia and the Pacific islands. The diverse geographical environments have led to the emergence of many unique and endangered species, although there is limited genomic information available about them. In this study, we generated high-quality reference genomes for three endangered species: two that are endemic to Hawai'i, Polyscias cf. bisattenuata and Polyscias lallanii, and one more widespread species, Polyscias macgillivrayi. We identified a total of 51,083, 60,881, and 29,060 genes in these three species, respectively. Whole-genome duplication analysis indicated that all three species underwent a common duplication event. By examining the phylogenetic and structural characteristics of the terpene synthase gene family in these species and closely related species, we identified several gene clusters that play crucial roles in metabolite synthesis. A variety of mono- and sesquiterpenoids were detected, with several of these compounds having been validated in previous studies. Our findings provide a foundation for further genetic and biochemical investigations of Polyscias, which may aid in the conservation of these endangered species.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"18 1","pages":"e20563"},"PeriodicalIF":3.9,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11839933/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143460204","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":"An organ-specific transcriptome atlas of Curcuma wenyujin: MicroRNAs, phasiRNAs, and metabolic pathways.","authors":"Xiaoxia Ma, Yinju Tang, Zedi Feng, Xiu Yin, Yijun Meng, Xiaopu Yin, Tian Xie","doi":"10.1002/tpg2.20564","DOIUrl":"10.1002/tpg2.20564","url":null,"abstract":"<p><p>Curcuma wenyujin Y. H. Chen et C. Ling (C. wenyujin) is a medicinal plant widely used for clinical treatments. In this study, integrated omics data analyses enabled us to discover the microRNAs (miRNAs) and the phased small interfering RNAs (phasiRNAs) on a transcriptome-wide scale. A total of 186 mature miRNAs and 23 precursors were reported. Besides, 31 miRNAs of 14 families were organ-specifically expressed, and 13 of these miRNAs could perform organ-specific target regulation. More than 80% of the phasiRNA loci were organ-specifically expressed, especially in tubers. In some cases, phasiRNAs with distinct increments, but with accordant organ-specific expression patterns, were generated from a highly overlapped region, indicating that different machineries might be synchronously engaged in phasiRNA processing. Based on the transcriptome assembly, 28 and 56 tuber-specific genes were identified to be involved in alkaloid and terpenoid metabolisms, respectively. Analysis of the enzyme-coding genes of the β-elemene biosynthetic pathway showed that the downstream genes were tuber-specific, while the upstream genes were not. We assumed that the precursor metabolites produced in the other organs might be delivered to the tubers for the final steps of β-elemene biosynthesis. Summarily, our report provided an organ-specific transcriptome atlas of C. wenyujin, which could serve as the basis for the molecular studies on organ development and secondary metabolisms in this plant.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"18 1","pages":"e20564"},"PeriodicalIF":3.9,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11806286/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143374775","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":"Translating weighted probabilistic bits to synthetic genetic circuits.","authors":"Matthew D Ciccone, Carlos D Messina","doi":"10.1002/tpg2.20525","DOIUrl":"10.1002/tpg2.20525","url":null,"abstract":"<p><p>Synthetic genetic circuits in plants could be the next technological horizon in plant breeding, showcasing potential for precise patterned control over expression. Nevertheless, uncertainty in metabolic environments prevents robust scaling of traditional genetic circuits for agricultural use, and studies show that a deterministic system is at odds with biological randomness. We analyze the necessary requirements for assuring Boolean logic gate sequences can function in unpredictable intracellular conditions, followed by interpreted pathways by which a mathematical representation of probabilistic circuits can be translated to biological implementation. This pathway is utilized through translation of a probabilistic circuit model presented by Pervaiz that works through a series of bits; each composed of a weighted matrix that reads inputs from the environment and a random number generator that takes the matrix as bias and outputs a positive or negative signal. The weighted matrix can be biologically represented as the regulatory elements that affect transcription near promotors, allowing for an electrical bit to biological bit translation that can be refined through tuning using invertible logic prediction of the input to output relationship of a genetic response. Failsafe mechanisms should be introduced, possibly through the use of self-eliminating CRISPR-Cas9, dosage compensation, or cybernetic modeling (where CRISPR is clustered regularly interspaced short palindromic repeats and Cas9 is clustered regularly interspaced short palindromic repeat-associated protein 9). These safety measures are needed for all biological circuits, and their implementation is needed alongside work with this specific model. With applied responses to external factors, these circuits could allow fine-tuning of organism adaptation to stress while providing a framework for faster complex expression design in the field.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20525"},"PeriodicalIF":3.9,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11726414/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142478530","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":"Sparse testing designs for optimizing resource allocation in multi-environment cassava breeding trials.","authors":"Nelson Lubanga, Beatrice E Ifie, Reyna Persa, Ibnou Dieng, Ismail Yusuf Rabbi, Diego Jarquin","doi":"10.1002/tpg2.20558","DOIUrl":"10.1002/tpg2.20558","url":null,"abstract":"<p><p>The development of improved cultivars requires establishing multi-environment trials (METs) to evaluate their performance under a wide range of environmental conditions. However, the high phenotyping costs often limit the capacity to evaluate genotypes in all the target environments. Our main objective was to explore the potential of implementing sparse testing in cassava breeding programs to reduce the cost of phenotyping in METs. The population used in this study consisted of 435 cassava genotypes evaluated in five environments in Nigeria for dry matter (dm) and fresh root yield (fyld). Sparse testing designs were developed based on non-overlapping (NOL), completely overlapping (OL), and intermediates between NOL and OL genotypes. Three prediction models were assessed (one based on phenotypes only, while two had genomic data). All the three models had a higher predictive ability and a lower mean square error (MSE) when a large training set was used. Predictive ability increased and MSE reduced when genotype-by-environment interaction (G × E) was modeled for the same training set sizes and allocations. Predictive ability decreased while MSE increased with the increasing OL genotypes across the environments, suggesting that only a few OL genotypes may be required to set up METs for model training. Sparse testing using a model incorporating G × E could be implemented to reduce cost of phenotyping in cassava METs. If data were available, integrating crop growth models (CGMs) with genomic prediction holds the potential to improve predictive ability. The training population used for sparse testing could be optimized to determine the optimal size and distribution of genotypes to increase the predictive ability and reduce cost under a fixed budget.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"18 1","pages":"e20558"},"PeriodicalIF":3.9,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11800058/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143256956","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 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":"<p><p>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.</p>","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}

{"title":"A graph model for genomic prediction in the context of a linear mixed model framework.","authors":"Osval A Montesinos-López, Gloria Isabel Huerta Prado, José Cricelio Montesinos-López, Abelardo Montesinos-López, José Crossa","doi":"10.1002/tpg2.20522","DOIUrl":"10.1002/tpg2.20522","url":null,"abstract":"<p><p>Genomic selection is revolutionizing both plant and animal breeding, with its practical application depending critically on high prediction accuracy. In this study, we aimed to enhance prediction accuracy by exploring the use of graph models within a linear mixed model framework. Our investigation revealed that incorporating the graph constructed with line connections alone resulted in decreased prediction accuracy compared to conventional methods that consider only genotype effects. However, integrating both genotype effects and the graph structure led to slightly improved results over considering genotype effects alone. These findings were validated across 14 datasets commonly used in plant breeding research.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20522"},"PeriodicalIF":3.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11628911/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142382136","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 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":"<p><p>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.</p>","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}

{"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":"<p><p>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.</p>","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}