Dataset Information

Phytochrome Interacting Factors (PIFs) in Solanum lycopersicum: Diversity, Evolutionary History and Expression Profiling during Different Developmental Processes.

ABSTRACT: Although the importance of light for tomato plant yield and edible fruit quality is well known, the PHYTOCHROME INTERACTING FACTORS (PIFs), main components of phytochrome-mediated light signal transduction, have been studied almost exclusively in Arabidopsis thaliana. Here, the diversity, evolution and expression profile of PIF gene subfamily in Solanum lycopersicum was characterized. Eight tomato PIF loci were identified, named SlPIF1a, SlPIF1b, SlPIF3, SlPIF4, SlPIF7a, SlPIF7b, SlPIF8a and SlPIF8b. The duplication of SlPIF1, SlPIF7 and SlPIF8 genes were dated and temporally coincided with the whole-genome triplication event that preceded tomato and potato divergence. Different patterns of mRNA accumulation in response to light treatments were observed during seedling deetiolation, dark-induced senescence, diel cycle and fruit ripening. SlPIF4 showed similar expression profile as that reported for A. thaliana homologs, indicating an evolutionary conserved function of PIF4 clade. A comprehensive analysis of the evolutionary and transcriptional data allowed proposing that duplicated SlPIFs have undergone sub- and neofunctionalization at mRNA level, pinpointing the importance of transcriptional regulation for the maintenance of duplicated genes. Altogether, the results indicate that genome polyploidization and functional divergence have played a major role in diversification of the Solanum PIF gene subfamily.

SUBMITTER: Rosado D

PROVIDER: S-EPMC5089782 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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Phytochrome Interacting Factors (PIFs) in Solanum lycopersicum: Diversity, Evolutionary History and Expression Profiling during Different Developmental Processes.

Rosado Daniele D Gramegna Giovanna G Cruz Aline A Lira Bruno Silvestre BS Freschi Luciano L de Setta Nathalia N Rossi Magdalena M

PloS one 20161101 11

Although the importance of light for tomato plant yield and edible fruit quality is well known, the PHYTOCHROME INTERACTING FACTORS (PIFs), main components of phytochrome-mediated light signal transduction, have been studied almost exclusively in Arabidopsis thaliana. Here, the diversity, evolution and expression profile of PIF gene subfamily in Solanum lycopersicum was characterized. Eight tomato PIF loci were identified, named SlPIF1a, SlPIF1b, SlPIF3, SlPIF4, SlPIF7a, SlPIF7b, SlPIF8a and SlP ...[more]

PMID: 27802334

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Project description:BACKGROUND: The natural phenotypic variability present in the germplasm of cultivated plants can be linked to molecular polymorphisms using association genetics. However it is necessary to consider the genetic structure of the germplasm used to avoid false association. The knowledge of genetic structure of plant populations can help in inferring plant evolutionary history. In this context, we genotyped 360 wild, feral and cultivated accessions with 20 simple sequence repeat markers and investigated the extent and structure of the genetic variation. The study focused on the red fruited tomato clade involved in the domestication of tomato and confirmed the admixture status of cherry tomatoes (Solanum lycopersicum var. cerasiforme). We used a nested sample strategy to set-up core collection maximizing the genetic diversity with a minimum of individuals. RESULTS: Molecular diversity was considerably lower in S. lycopersicum i.e. the domesticated form. Model-based analysis showed that the 144 S. lycopersicum var. cerasiforme accessions were structured into two groups: one close to the domesticated group and one resulting from the admixture of the S. lycopersicum and S. pimpinellifolium genomes. SSR genotyping also indicates that domesticated and wild tomatoes have evolved as a species complex with intensive level of hybridization. We compiled genotypic and phenotypic data to identify sub-samples of 8, 24, 32 and 64 cherry tomato accessions that captured most of the genetic and morphological diversity present in the entire S. lycopersicum var. cerasiforme collection. CONCLUSION: The extent and structure of allelic variation is discussed in relation to historical events like domestication and modern selection. The potential use of the admixed group of S. lycopersicum var. cerasiforme for association genetics studies is also discussed. Nested core collections sampled to represent tomato diversity will be useful in diversity studies. Molecular and phenotypic variability of these core collections is defined. These collections are available for the scientific community and can be used as standardized panels for coordinating efforts on identifying novel interesting genes and on examining the domestication process in more detail.

Project description:Seeds germination and seedlings growth of Cucumis sativus and Solanum lycopersicum were monitored in in vitro and in vivo experiments after application of different concentrations of NaCl (25, 50, 100 and 200 mM). Photosynthetic pigments content and the biochemical responses of C. sativus and S. lycopersicum were assessed. Salinity stress slightly delayed the seeds germination rate and significantly reduced the percentage of germination as well as shoot length under the highest salt concentration (200 mM) in cucumber. Furthermore, root length was decreased significantly in all treatments. Whereas, in tomato, a prominent delay in seeds germination rate, the germination percentage and seedlings growth (shoot and root lengths) were significantly influenced under all concentrations of NaCl. Fresh and dry weights were reduced prominently in tomato compared to cucumber. Photosynthetic pigments content was reduced but with pronounced decreasing in tomato compared to cucumber. Secondary metabolites profiling in both plants under stress was varied from tomato to cucumber. The content of saponins, proline and total antioxidant capacity was reduced more prominently in tomato as compared to cucumber. On the other hand, the content of phenolics and flavonoids was increased in both plants with pronounced increase in tomato particularly under the highest level of salinity stress. The metabolomic profiling in stressful plants was significantly influenced by salinity stress and some bioactive secondary metabolites was enhanced in both cucumber and tomato plants. The enhancement of secondary metabolites under salinity stress may explain the tolerance and sensitivity of cucumber and tomato under salinity stress. The metabolomic evaluation combined with multivariate data analysis revealed a similar mechanism of action of plants to mediate stress, with variant level of this response in both plant species. Based on these results, the effect of salinity stress on seeds germination, seedlings growth and metabolomic content of plants was discussed in terms of tolerance and sensitivity of plants to salinity stress.

Dataset Information

Phytochrome Interacting Factors (PIFs) in Solanum lycopersicum: Diversity, Evolutionary History and Expression Profiling during Different Developmental Processes.

Publications

Phytochrome Interacting Factors (PIFs) in Solanum lycopersicum: Diversity, Evolutionary History and Expression Profiling during Different Developmental Processes.

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