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A roadmap for functional structural variants in the soybean genome.

ABSTRACT: Gene structural variation (SV) has recently emerged as a key genetic mechanism underlying several important phenotypic traits in crop species. We screened a panel of 41 soybean (Glycine max) accessions serving as parents in a soybean nested association mapping population for deletions and duplications in more than 53,000 gene models. Array hybridization and whole genome resequencing methods were used as complementary technologies to identify SV in 1528 genes, or approximately 2.8%, of the soybean gene models. Although SV occurs throughout the genome, SV enrichment was noted in families of biotic defense response genes. Among accessions, SV was nearly eightfold less frequent for gene models that have retained paralogs since the last whole genome duplication event, compared with genes that have not retained paralogs. Increases in gene copy number, similar to that described at the Rhg1 resistance locus, account for approximately one-fourth of the genic SV events. This assessment of soybean SV occurrence presents a target list of genes potentially responsible for rapidly evolving and/or adaptive traits.

SUBMITTER: Anderson JE

PROVIDER: S-EPMC4455779 | biostudies-literature | 2014 May

REPOSITORIES: biostudies-literature

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A roadmap for functional structural variants in the soybean genome.

Anderson Justin E JE Kantar Michael B MB Kono Thomas Y TY Fu Fengli F Stec Adrian O AO Song Qijian Q Cregan Perry B PB Specht James E JE Diers Brian W BW Cannon Steven B SB McHale Leah K LK Stupar Robert M RM

G3 (Bethesda, Md.) 20140522 7

Gene structural variation (SV) has recently emerged as a key genetic mechanism underlying several important phenotypic traits in crop species. We screened a panel of 41 soybean (Glycine max) accessions serving as parents in a soybean nested association mapping population for deletions and duplications in more than 53,000 gene models. Array hybridization and whole genome resequencing methods were used as complementary technologies to identify SV in 1528 genes, or approximately 2.8%, of the soybea ...[more]

PMID: 24855315

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Project description:IntroductionPatients with ventricular tachyarrhythmias (VT) are at high risk of sudden cardiac death. When appropriate, catheter ablation is modestly effective, with relatively high VT recurrence and complication rates. Personalized models that incorporate imaging and computational approaches have advanced VT management. However, 3D patient-specific functional electrical information is typically not considered. We hypothesize that incorporating non-invasive 3D electrical and structural characterization in a patient-specific model improves VT-substrate recognition and ablation targeting.Materials and methodsIn a 53-year-old male with ischemic cardiomyopathy and recurrent monomorphic VT, we built a structural-functional model based on high-resolution 3D late-gadolinium enhancement (LGE) cardiac magnetic resonance imaging (3D-LGE CMR), multi-detector computed tomography (CT), and electrocardiographic imaging (ECGI). Invasive data from high-density contact and pace mapping obtained during endocardial VT-substrate modification were also incorporated. The integrated 3D electro-anatomic model was analyzed off-line.ResultsMerging the invasive voltage maps and 3D-LGE CMR endocardial geometry led to a mean Euclidean node-to-node distance of 5 ± 2 mm. Inferolateral and apical areas of low bipolar voltage (<1.5 mV) were associated with high 3D-LGE CMR signal intensity (>0.4) and with higher transmurality of fibrosis. Areas of functional conduction delay or block (evoked delayed potentials, EDPs) were in close proximity to 3D-LGE CMR-derived heterogeneous tissue corridors. ECGI pinpointed the epicardial VT exit at ∼10 mm from the endocardial site of origin, both juxtaposed to the distal ends of two heterogeneous tissue corridors in the inferobasal left ventricle. Radiofrequency ablation at the entrances of these corridors, eliminating all EDPs, and at the VT site of origin rendered the patient non-inducible and arrhythmia-free until the present day (20 months follow-up). Off-line analysis in our model uncovered dynamic electrical instability of the LV inferolateral heterogeneous scar region which set the stage for an evolving VT circuit.Discussion and conclusionWe developed a personalized 3D model that integrates high-resolution structural and electrical information and allows the investigation of their dynamic interaction during arrhythmia formation. This model enhances our mechanistic understanding of scar-related VT and provides an advanced, non-invasive roadmap for catheter ablation.

Project description:Background and aimsTurgor pressure within a plant cell represents the key to the mechanistical descriptiion of plant growth, combining the effects of both water and carbon availability. The high level of spatio-temporal variation and diurnal dynamics in turgor pressure within a single plant make it a challenge to model these on the fine spatial scale required for functional-structural plant models (FSPMs). A conceptual model for turgor-driven growth in FSPMs has been established previously, but its practical use has not yet been explored.MethodsA turgor-driven growth model was incorporated in a newly established FSPM for soybean. The FSPM simulates dynamics in photosynthesis, transpiration and turgor pressure in direct relation to plant growth. Comparisons of simulations with field data were used to evaluate the potential and shortcomings of the modelling approach.Key resultsModel simulations revealed the need to include an initial seed carbon contribution, a more realistic sink function, an estimation of respiration, and the distinction between osmotic and structural sugars, in order to achieve a realistic model of plant growth. However, differences between simulations and observations remained in individual organ growth patterns and under different environmental conditions. This exposed the need to further investigate the assumptions of developmental and environmental (in)sensitivity of the parameters, which represent physiological and biophysical organ properties in the model, in future research.ConclusionsThe model in its current form is primarily a diagnostic tool, to better understand and model the behaviour of water relations on the scale of individual plant organs throughout the plant life cycle. Potential future applications include its use as a phenotyping tool to capture differences in plant performance between genotypes and growing environments in terms of specific plant characteristics. Additionally, focused experiments can be used to further improve the model mechanisms to lead to better predictive FSPMs, including scenarios of water deficit.

Dataset Information

A roadmap for functional structural variants in the soybean genome.

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A roadmap for functional structural variants in the soybean genome.

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