Dataset Information

Quantifying the importance of a realistic tomato (Solanum lycopersicum) leaflet shape for 3-D light modelling.

ABSTRACT:

Background and aims

Leaflet shapes of tomato plants (Solanum lycopersicum) have been reduced to simple geometric shapes in previous functional-structural plant models (FSPMs) in order to facilitate measurements and reduce the time required to reconstruct the plant virtually. The level of error that such simplifications introduce remains unaddressed. This study therefore aims to quantify the modelling error associated with simplifying leaflet shapes.

Methods

Realistic shapes were implemented in a static tomato FSPM based on leaflet scans, and simulation results were compared to simple geometric shapes used in previous tomato FSPMs in terms of light absorption and gross photosynthesis, for both a single plant and a glasshouse scenario.

Key results

The effect of simplifying leaflet shapes in FSPMs leads to small but significant differences in light absorption, alterations of canopy light conditions and differences in photosynthesis. The magnitude of these differences depends on both the type of leaflet shape simplification used and the canopy shape and density. Incorporation of realistic shapes requires a small increase in initial measurement and modelling work to establish a shape database and comes at the cost of a slight increase in computation time.

Conclusions

Our findings indicate that the error associated with leaflet shape simplification is small, but often unpredictable, and is affected by plant structure but also lamp placement, which is often a primary optimization goal of these static models. Assessment of the cost-benefit of realistic shape inclusion shows relatively little drawbacks for a decrease in model uncertainty.

SUBMITTER: Vermeiren J

PROVIDER: S-EPMC7489060 | biostudies-literature | 2020 Sep

REPOSITORIES: biostudies-literature

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Publications

Quantifying the importance of a realistic tomato (Solanum lycopersicum) leaflet shape for 3-D light modelling.

Vermeiren Jonathan J Villers Selwyn L Y SLY Wittemans Lieve L Vanlommel Wendy W van Roy Jeroen J Marien Herman H Coussement Jonas R JR Steppe Kathy K

Annals of botany 20200901 4

<h4>Background and aims</h4>Leaflet shapes of tomato plants (Solanum lycopersicum) have been reduced to simple geometric shapes in previous functional-structural plant models (FSPMs) in order to facilitate measurements and reduce the time required to reconstruct the plant virtually. The level of error that such simplifications introduce remains unaddressed. This study therefore aims to quantify the modelling error associated with simplifying leaflet shapes.<h4>Methods</h4>Realistic shapes were i ...[more]

PMID: 31840158

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Project description:BackgroundEndogenous pararetroviral sequences (EPRVs) are a recently discovered class of repetitive sequences that is broadly distributed in the plant kingdom. The potential contribution of EPRVs to plant pathogenicity or, conversely, to virus resistance is just beginning to be explored. Some members of the family Solanaceae are particularly rich in EPRVs. In previous work, EPRVs have been characterized molecularly in various species of Nicotiana including N.tabacum (tobacco) and Solanum tuberosum (potato). Here we describe a family of EPRVs in cultivated tomato (Solanum lycopersicum L.) and a wild relative (S.habrochaites).ResultsMolecular cloning and DNA sequence analysis revealed that tomato EPRVs (named LycEPRVs) are most closely related to those in tobacco. The sequence similarity of LycEPRVs in S.lycopersicum and S.habrochaites indicates they are potentially derived from the same pararetrovirus. DNA blot analysis revealed a similar genomic organization in the two species, but also some independent excision or insertion events after species separation, or flanking sequence divergence. LycEPRVs share with the tobacco elements a disrupted genomic structure and frequent association with retrotransposons. Fluorescence in situ hybridization revealed that copies of LycEPRV are dispersed on all chromosomes in predominantly heterochromatic regions. Methylation of LycEPRVs was detected in CHG and asymmetric CHH nucleotide groups. Although normally quiescent EPRVs can be reactivated and produce symptoms of infection in some Nicotiana interspecific hybrids, a similar pathogenicity of LycEPRVs could not be demonstrated in Solanum L. section Lycopersicon [Mill.] hybrids. Even in healthy plants, however, transcripts derived from multiple LycEPRV loci and short RNAs complementary to LycEPRVs were detected and were elevated upon infection with heterologous viruses encoding suppressors of PTGS.ConclusionThe analysis of LycEPRVs provides further evidence for the extensive invasion of pararetroviral sequences into the genomes of solanaceous plants. The detection of asymmetric CHH methylation and short RNAs, which are hallmarks of RNAi in plants, suggests that LycEPRVs are controlled by an RNA-mediated silencing mechanism.

Project description:BackgroundMany highly beneficial traits (e.g. disease or abiotic stress resistance) have been transferred into crops through crosses with their wild relatives. The 13 recognized species of tomato (Solanum section Lycopersicon) are closely related to each other and wild species genes have been extensively used for improvement of the crop, Solanum lycopersicum L. In addition, the lack of geographical barriers has permitted natural hybridization between S. lycopersicum and its closest wild relative Solanum pimpinellifolium in Ecuador, Peru and northern Chile. In order to better understand patterns of S. lycopersicum diversity, we sequenced 47 markers ranging in length from 130 to 1200 bp (total of 24 kb) in genotypes of S. lycopersicum and wild tomato species S. pimpinellifolium, Solanum arcanum, Solanum peruvianum, Solanum pennellii and Solanum habrochaites. Between six and twelve genotypes were comparatively analyzed per marker. Several of the markers had previously been hypothesized as carrying wild species alleles within S. lycopersicum, i.e., cryptic introgressions.ResultsEach marker was mapped with high confidence (e<1 x 10-30) to a single genomic location using BLASTN against tomato whole genome shotgun chromosomes (SL2.40) database. Neighbor-joining trees showed high mean bootstrap support (86.8 ± 2.34%) for distinguishing red-fruited from green-fruited taxa for 38 of the markers. Hybridization and parsimony splits networks, genomic map positions of markers relative to documented introgressions, and historical origins of accessions were used to interpret evolutionary patterns at nine markers with putatively introgressed alleles.ConclusionOf the 47 genetic markers surveyed in this study, four were involved in linkage drag on chromosome 9 during introgression breeding, while alleles at five markers apparently originated from natural hybridization with S. pimpinellifolium and were associated with primitive genotypes of S. lycopersicum. The positive identification of introgressed genes within crop species such as S. lycopersicum will help inform conservation and utilization of crop germplasm diversity, for example, facilitating the purging of undesirable linkage drag or the exploitation of novel, favorable alleles.

Dataset Information

Quantifying the importance of a realistic tomato (Solanum lycopersicum) leaflet shape for 3-D light modelling.

Background and aims

Methods

Key results

Conclusions

Publications

Quantifying the importance of a realistic tomato (Solanum lycopersicum) leaflet shape for 3-D light modelling.

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