Introgression shapes fruit color convergence in invasive Galapagos tomato.
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ABSTRACT:
SUBMITTER: Gibson MJ
PROVIDER: S-EPMC8294854 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:We performed transcriptome analyses throughout fruit development using the tomato cultivar M82 and its near-isogenic line IL8-3, with interesting and useful traits such as a high content of soluble solids. To identify genes that show differential expression between M82 and IL8-3 fruits, we used a custom microarray containing 43,803 tomato probes. Some genes, such as cell wall invertase and sucrose synthase genes, which are encoded by LIN6 (Solyc10g083290) and TOMSSF (Solyc12g009300) respectively, are well known to play a key role in the sink function of fruit. In this study, the levels of LIN6 and TOMSSF transcripts were higher in IL8-3 than in M82 fruit at 20 and 30 DAF, which are developmental stages for starch accumulation and increased hexose content, respectively, in IL8-3 fruit (Ikeda et al. 2013), and decreased to the level of M82 at ripening stage. Similar patterns were observed in many metabolites of glycolysis and the pentose phosphate pathway as well as metabolites in starch and sucrose metabolism.
2016-07-25 | GSE78260 | GEO
Project description:We performed transcriptome analyses throughout fruit development using the tomato cultivar M82 and its near-isogenic line IL8-3, with interesting and useful traits such as a high content of soluble solids. To identify genes that show differential expression between M82 and IL8-3 fruits, we used a custom microarray containing 43,803 tomato probes. Some genes, such as cell wall invertase and sucrose synthase genes, which are encoded by LIN6 (Solyc10g083290) and TOMSSF (Solyc12g009300) respectively, are well known to play a key role in the sink function of fruit. In this study, the levels of LIN6 and TOMSSF transcripts were higher in IL8-3 than in M82 fruit at 20 and 30 DAF, which are developmental stages for starch accumulation and increased hexose content, respectively, in IL8-3 fruit (Ikeda et al. 2013), and decreased to the level of M82 at ripening stage. Similar patterns were observed in many metabolites of glycolysis and the pentose phosphate pathway as well as metabolites in starch and sucrose metabolism. Gene expressions during fruit development were analyzed. Three biological replicates were prepared for each stage, and a total of 24 samples were analyzed.
2016-07-25 | E-GEOD-78260 | biostudies-arrayexpress
Project description:San Marzano (SM) is a traditional Italian landrace characterized by red elongated fruits, originating in the province of Naples (Italy) and cultivated worldwide. Three mutations, yellow flesh (r), green flesh (gf) and colorless fruit epidermis (y) were introduced into SM by backcross and the resulting introgression lines (ILs) produced the expected yellow, brown and pink fruit variants. In addition, ILs carrying double combinations of those mutations were obtained. The six ILs plus the SM reference were analyzed for volatile (VOC), non-polar (NP) and polar (P) metabolites. Sixty-eight VOCs were identified, and several differences evidenced in the ILs; overall gf showed epistasis over r and y and r over y. Analysis of the NP component identified 54 metabolites; variation in early carotenoids (up to lycopene) and chlorophylls characterized respectively the ILs containing r and gf. In addition, compounds belonging to the quinone and xanthophyll classes were present in genotypes carrying the r mutation at levels higher than SM. Finally, the analysis of 129 P metabolites evidenced different levels of vitamins, amino acids, lipids and phenylpropanoids in the ILs. A correlation network approach was used to investigate metabolite-metabolite relationships in the mutant lines. Altogether these differences potentially modified the hedonistic and nutritional value of the berry. In summary, single and combined mutations in gf, r and y generated interesting visual and compositional diversity in the SM landrace, while maintaining its original typology.
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Project description:Volatile organic compounds (VOCs) are major determinants of fruit flavor, a primary objective in tomato breeding. A recombinant inbred line (RIL) population consisting of 169 lines derived from a cross between Solanum lycopersicum and a red-fruited wild tomato species Solanum pimpinellifolium accession (SP) was characterized for VOCs in three different seasons. Correlation and hierarchical cluster analyses were performed on the 52 VOCs identified, providing a tool for the putative assignation of individual compounds to metabolic pathways. Quantitative trait locus (QTL) analysis, based on a genetic linkage map comprising 297 single nucleotide polymorphisms (SNPs), revealed 102 QTLs (75% not described previously) corresponding to 39 different VOCs. The SP alleles exerted a positive effect on most of the underlying apocarotenoid volatile QTLs-regarded as desirable for liking tomato-indicating that alleles inherited from SP are a valuable resource for flavor breeding. An introgression line (IL) population developed from the same parental genotypes provided 12 ILs carrying a single SP introgression and covering 85 VOC QTLs, which were characterized at three locations. The results showed that almost half of the QTLs previously identified in the RILs maintained their effect in an IL form, reinforcing the value of these QTLs for flavor/aroma breeding in cultivated tomato.
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Project description:WRKY transcription factors (TFs) play important roles in stress responses in planta. However, the function of WRKY TFs in the regulation of fruit ripening is unclear. Here, 23 tomato SlWRKYs that are similar to ethylene-responsive WRKY genes from other plant species, or show up-regulation during fruit ripening in previous genome-wide study, were selected, and their function in fruit ripening was investigated. Twelve SlWRKYs were found to be responsive to ethylene (SlER-WRKYs), showing expression patterns similar to those of genes related to fruit ripening. Eight SlER-WRKYs-SlWRKY16, 17, 22, 25, 31, 33, 53, and 54, detected in the nuclei-interacted with and activated the promoters of 4 genes related to color change: Pheophytin Pheophorbide Hydrolase (SlPPH), Pheophorbide a Oxygenase (SlPAO), Phytoene Synthase 1 (SlPSY1) and Phytoene Desaturase (SlPDS). Yeast two-hybrid and bimolecular fluorescence complement (BiFC) assays in Arabidopsis protoplasts indicated that protein interactions occurred between SlWRKY17 and SlRIN, SlERF2b or SlERF7; SlWRKY33 and SlERF7; SlWRKY54 and SlERF2b; and SlWRKY16 and SlWRKY17. Suppression of SlWRKY 16, 17, 53 or 54 by virus-induced gene silencing (VIGS) retarded the red coloration of the fruit. Our study provides comprehensive molecular evidence that WRKY TFs function in fruit ripening, particularly in color change, and are linked to the intricate regulatory network of other ripening regulators.
| S-EPMC5709409 | biostudies-literature
Project description:We have studied a genomic library of introgression lines from the Solanum pimpinellifolium accession TO-937 into the genetic background of the "Moneymaker" cultivar in order to evaluate the accession's breeding potential. Overall, no deleterious phenotypes were observed, and the plants and fruits were phenotypically very similar to those of "Moneymaker," which confirms the feasibility of translating the current results into elite breeding programs. We identified chromosomal regions associated with traits that were both vegetative (plant vigor, trichome density) and fruit-related (morphology, organoleptic quality, color). A trichome-density locus was mapped on chromosome 10 that had not previously been associated with insect resistance, which indicates that the increment of trichomes by itself does not confer resistance. A large number of quantitative trait loci (QTLs) have been identified for fruit weight. Interestingly, fruit weight QTLs on chromosomes 1 and 10 showed a magnitude effect similar to that of QTLs previously defined as important in domestication and diversification. Low variability was observed for fruit-shape-related traits. We were, however, able to identify a QTL for shoulder height, although the effects were quite low, thus demonstrating the suitability of the current population for QTL detection. Regarding organoleptic traits, consistent QTLs were detected for soluble solid content (SSC). Interestingly, QTLs on chromosomes 2 and 9 increased SSC but did not affect fruit weight, making them quite promising for introduction in modern cultivars. Three ILs with introgressions on chromosomes 1, 2, and 10 increased the internal fruit color, making them candidates for increasing the color of modern cultivars. Comparing the QTL detection between this IL population and a recombinant inbred line population from the same cross, we found that QTL stability across generations depended on the trait, as it was very high for fruit weight but low for organoleptic traits. This difference in QTL stability may be due to a predominant additive gene action for QTLs involved in fruit weight, whereas epistatic and genetic background interactions are most likely important for the other traits.
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Project description:While it is appreciated that population size changes can impact patterns of deleterious variation in natural populations, less attention has been paid to how gene flow affects and is affected by the dynamics of deleterious variation. Here we use population genetic simulations to examine how gene flow impacts deleterious variation under a variety of demographic scenarios, mating systems, dominance coefficients, and recombination rates. Our results show that admixture between populations can temporarily reduce the genetic load of smaller populations and cause increases in the frequency of introgressed ancestry, especially if deleterious mutations are recessive. Additionally, when fitness effects of new mutations are recessive, between-population differences in the sites at which deleterious variants exist creates heterosis in hybrid individuals. Together, these factors lead to an increase in introgressed ancestry, particularly when recombination rates are low. Under certain scenarios, introgressed ancestry can increase from an initial frequency of 5% to 30-75% and fix at many loci, even in the absence of beneficial mutations. Further, deleterious variation and admixture can generate correlations between the frequency of introgressed ancestry and recombination rate or exon density, even in the absence of other types of selection. The direction of these correlations is determined by the specific demography and whether mutations are additive or recessive. Therefore, it is essential that null models of admixture include both demography and deleterious variation before invoking other mechanisms to explain unusual patterns of genetic variation.
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Project description:Genetic improvement of tomato by targeted control of fruit softening. Uluisik et al. Nature Biotechnology (2016) doi:10.1038/nbt.3602
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Project description:The cuticle is a specialized cell wall layer that covers the outermost surface of the epidermal cells and has important implications for fruit permeability and pathogen susceptibility. In order to decipher the genetic control of tomato fruit cuticle composition, an introgression line (IL) population derived from a biparental cross between Solanum pennellii (LA0716) and the Solanum lycopersicum cultivar M82 was used to build a first map of associated quantitative trait loci (QTLs). A total of 24 cuticular waxes and 26 cutin monomers were determined. They showed changes associated with 18 genomic regions distributed in nine chromosomes affecting 19 ILs. Out of the five main fruit cuticular components described for the wild species S. pennellii, three of them were associated with IL3.4, IL12.1, and IL7.4.1, causing an increase in n-alkanes (≥C30), a decrease in amyrin content, and a decrease in cuticle thickness of ~50%, respectively. Moreover, we also found a QTL associated with increased levels of amyrins in IL3.4. In addition, we propose some candidate genes on the basis of their differential gene expression and single nucleotide polymorphism variability between the introgressed and the recurrent alleles, which will be the subjects of further investigation.
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Project description:IntroductionThe primary metabolism of plants, which is mediated by nitrogen, is closely related to the defense response to insect herbivores.MethodsAn experimental system was established to examine how nitrogen mediated tomato resistance to an insect herbivore, the oriental fruit fly (Bactrocera dorsalis). All tomatoes were randomly assigned to the suitable nitrogen (control, CK) treatment, nitrogen excess (NE) treatment and nitrogen deficiency (ND) treatment.ResultsWe found that nitrogen excess significantly increased the aboveground biomass of tomato and increased the pupal biomass of B. dorsalis. Metabolome analysis showed that nitrogen excess promoted the biosynthesis of amino acids in healthy fruits, including γ-aminobutyric acid (GABA), arginine and asparagine. GABA was not a differential metabolite induced by injury by B. dorsalis under nitrogen excess, but it was significantly induced in infested fruits at appropriate nitrogen levels. GABA supplementation not only increased the aboveground biomass of plants but also improved the defensive response of tomato.DiscussionThe biosynthesis of GABA in tomato is a resistance response to feeding by B. dorsalis in appropriate nitrogen, whereas nitrogen excess facilitates the pupal weight of B. dorsalis by inhibiting synthesis of the GABA pathway. This study concluded that excess nitrogen inhibits tomato defenses in plant-insect interactions by inhibiting GABA synthesis, answering some unresolved questions about the nitrogen-dependent GABA resistance pathway to herbivores.
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