Expression profile analysis of early fruit development in iaaM-parthenocarpic tomato plants

<p>Abstract</p> <p>Background</p> <p>Fruit normally develops from the ovary after pollination and fertilization. However, the ovary can also generate seedless fruit without fertilization by parthenocarpy. Parthenocarpic fruit development has been obtained in tomato (<it>Solanum lycopersicum</it>) by genetic modification using auxin-synthesising gene(s) (<it>DefH9-iaaM</it>; <it>DefH9-RI-iaaM</it>) expressed specifically in the placenta and ovules.</p> <p>Findings</p> <p>We have performed a cDNA Amplified Fragment Length Polymorphism (cDNA-AFLP) analysis on pre-anthesis tomato flower buds (0.5 cm long) collected from <it>DefH9-iaaM </it>and <it>DefH9-RI-iaaM </it>parthenocarpic and wild-type plants, with the aim to identify genes involved in very early phases of tomato fruit development. We detected 212 transcripts differentially expressed in auxin-ipersynthesising pre-anthesis flower buds, 65 of them (31%) have unknown function. Several differentially expressed genes show homology to genes involved in protein trafficking and protein degradation via proteasome. These processes are crucial for auxin cellular transport and signaling, respectively.</p> <p>Conclusion</p> <p>The data presented might contribute to elucidate the molecular basis of the fruiting process and to develop new methods to confer parthenocarpy to species of agronomic interest. In a recently published work, we have demonstrated that one of the genes identified in this screening, corresponding to #109 cDNA clone, regulates auxin-dependent fruit initiation and its suppression causes parthenocarpic fruit development in tomato.</p

Hybrids and allied species as potential rootstocks for eggplant: Effect of grafting on vigour, yield and overall fruit quality traits

Grafting of fruiting vegetables is an effective technique to overcome pests and diseases in modern cropping systems and it is often used to improve yield and fruit quality. Eggplant is an important vegetable crop that benefits significantly from grafting. In this regards, the exploitation, valorization and breeding of new rootstock genotypes as possible substitute to those commonly used (Solanum torvum and tomato hybrids) would permit an intensive eggplant crop system in those situations where a rootstock rotation is required. In the present article, we study the effects of several potential rootstocks including both wild/allied species of eggplant [S. torvum (STO), S. macrocarpon (SMA), S. aethiopicum (accession SASI), S. aethiopicum (accession SASa2), S. paniculatum (jurubeba) (SPA) and S. indicum (SIN)] and Msa 2/2 E7 and 460 CAL. eggplant hybrids on plant vigor, yield and fruit characteristics of eggplant F1 hybrid (‘Birgah’), in two spring-summer growing seasons (2014 and 2015). SPA and the hybrids Msa 2/2 E7 and 460 CAL. displayed a high percentage of grafting success. ‘Birgah’ scion grafted onto the two above-mentioned rootstocks showed a notable vigour and yield. Both rootstocks did not promote any unfavorable effects on apparent fruit quality traits and overall fruit composition. Furthermore, the concentration of glycoalkaloids in the fruit remained below the recommended safety value (200 mg/100 g of dw). These results suggest that SPA and Msa 2/2 E7 and 460 CAL. eggplant hybrids might represent a potential rootstock alternative to S. torvum

Mapping quantitative trait loci affecting biochemical and morphological fruit properties in eggplant (Solanum melongena L.)

Eggplant berries are a source of health-promoting metabolites including antioxidant and nutraceutical compounds, mainly anthocyanins and chlorogenic acid; however, they also contain some anti-nutritional compounds such as steroidal glycoalkaloids (SGA) and saponins, which are responsible for the bitter taste of the flesh and with potential toxic effects on humans. Up to now, Quantitative Trait Loci (QTL) for the metabolic content are far from being characterized in eggplant, thus hampering the application of breeding programs aimed at improving its fruit quality. Here we report on the identification of some QTL for the fruit metabolic content in an F2 intraspecific mapping population of 156 individuals, obtained by crossing the eggplant breeding lines ‘305E40’ x ‘67/3’. The same population was previously employed for the development of a RAD-tag based linkage map and the identification of QTL associated to morphological and physiological traits. The mapping population was biochemically characterized for both fruit basic qualitative data, like dry matter, °Brix, sugars and organic acids, as well as for health-related compounds such chlorogenic acid, (the main flesh monomeric phenol), the two peel anthocyanins (i.e. delphinidin-3-rutinoside (D3R) and delphinidin-3-(p-coumaroylrutinoside)-5-glucoside (nasunin)) and the two main steroidal glycoalkaloids, solasonine and solamargine. For most of the traits, one major QTL (PVE ≥ 10%) was spotted and putative orthologies with other Solanaceae crops are discussed. The present results supply valuable information to eggplant breeders on the inheritance of key fruit quality traits, thus providing potential tools to assist future breeding programs

A PLENA-like gene of peach is involved in carpel formation and subsequent transformation into a fleshy fruit

MADS-box genes have been shown to play a role in the formation of fruits, both in Arabidopsis and in tomato. In peach, two C-class MADS-box genes have been isolated. Both of them are expressed during flower and mesocarp development. Here a detailed analysis of a gene that belongs to the PLENA subfamily of MADS-box genes is shown. The expression of this PLENA-like gene (PpPLENA) increases during fruit ripening, and its ectopic expression in tomato plants causes the transformation of sepals into carpel-like structures that become fleshy and ripen like real fruits. Interestingly, the transgenic berries constitutively expressing the PpPLENA gene show an accelerated ripening, as judged by the expression of genes that are important for tomato fruit ripening. It is suggested that PpPLENA might interfere with the endogenous activity of TAGL1, thereby activating the fruit ripening pathway earlier compared with wild-type tomato plants

Identification of SNP and SSR markers in eggplant using RAD tag sequencing

<p>Abstract</p> <p>Background</p> <p>The eggplant (<it>Solanum melongena </it>L.) genome is relatively unexplored, especially compared to those of the other major <it>Solanaceae </it>crops tomato and potato. In particular, no SNP markers are publicly available; on the other hand, over 1,000 SSR markers were developed and publicly available. We have combined the recently developed Restriction-site Associated DNA (RAD) approach with Illumina DNA sequencing for rapid and mass discovery of both SNP and SSR markers for eggplant.</p> <p>Results</p> <p>RAD tags were generated from the genomic DNA of a pair of eggplant mapping parents, and sequenced to produce ~17.5 Mb of sequences arrangeable into ~78,000 contigs. The resulting non-redundant genomic sequence dataset consisted of ~45,000 sequences, of which ~29% were putative coding sequences and ~70% were in common between the mapping parents. The shared sequences allowed the discovery of ~10,000 SNPs and nearly 1,000 indels, equivalent to a SNP frequency of 0.8 per Kb and an indel frequency of 0.07 per Kb. Over 2,000 of the SNPs are likely to be mappable via the Illumina GoldenGate assay. A subset of 384 SNPs was used to successfully fingerprint a panel of eggplant germplasm, producing a set of informative diversity data. The RAD sequences also included nearly 2,000 putative SSRs, and primer pairs were designed to amplify 1,155 loci.</p> <p>Conclusion</p> <p>The high throughput sequencing of the RAD tags allowed the discovery of a large number of DNA markers, which will prove useful for extending our current knowledge of the genome organization of eggplant, for assisting in marker-aided selection and for carrying out comparative genomic analyses within the <it>Solanaceae </it>family.</p

Optimisation of transgene action at the post-transcriptional level: high quality parthenocarpic fruits in industrial tomatoes

Abstract Background Genetic engineering of parthenocarpy confers to horticultural plants the ability to produce fruits under environmental conditions that curtail fruit productivity and quality. The DefH9-iaaM transgene, whose predicted action is to confer auxin synthesis specifically in the placenta, ovules and derived tissues, has been shown to confer parthenocarpy to several plant species (tobacco, eggplant, tomato) and varieties. Results UC82 tomato plants, a typical cultivar used by the processing industry, transgenic for the DefH9-iaaM gene produce parthenocarpic fruits that are malformed. UC82 plants transgenic for the DefH9-RI-iaaM, a DefH9-iaaM derivative gene modified in its 5'ULR by replacing 53 nucleotides immediately upstream of the AUG initiation codon with an 87 nucleotides-long sequence derived from the rolA intron sequence, produce parthenocarpic fruits of high quality. In an in vitro translation system, the iaaM mRNA, modified in its 5'ULR is translated 3–4 times less efficiently than the original transcript. An optimal expressivity of parthenocarpy correlates with a reduced transgene mRNA steady state level in DefH9-RI-iaaM flower buds in comparison to DefH9-iaaM flower buds. Consistent with the known function of the iaaM gene, flower buds transgenic for the DefH9-RI-iaaM gene contain ten times more IAA than control untransformed flower buds, but five times less than DefH9-iaaM flower buds. Conclusions By using an auxin biosynthesis transgene downregulated at the post-transcriptional level, an optimal expressivity of parthenocarpy has been achieved in a genetic background not suitable for the original transgene. Thus, the method allows the generation of a wider range of expressivity of the desired trait in transgenic plants.</p

Molecular insights on the role of Arabidopsis thaliana NAOD in fruit set

Ornithine (Orn), an intermediate of arginine and polyamines (PAs) biosynthetic pathways, is produced in plants by N2-acetylornithine:Nacetylglutamate acetyltransferase (NAOGAcT). In enteric bacteria, Orn is synthesised also by N-acetylornithine deacetylase (NAOD) via a linear pathway. The plants seem to be unable to use this pathway despite the presence of many NAOD-like genes identified in various plant species. We have studied the role of the putative NAOD of Arabidopsis (At4g17830) by analysing the effects of its downregulation in vivo. AtNAOD-suppressed plants displayed an impaired fruit setting. AtNAOD downregulation determined a reduced Orn content and altered PAs levels. To elucidate the role of AtNAOD in fruit setting, we compared the mRNA profile of fertilised flowers of AtNAOD-downregulated plants with that of wild-type. We found 63 genes significantly changed (fold change 65 |2|). Our analysis revealed that the altered Orn and PAs metabolism in the reproductive organs of the AtNAOD-downregulated plants is associated with an impaired transcription of cysteine-rich signalling peptides involved in male-female cross-talk and perturbation of genes involved in regulating N:C status

The Arabidopsis N-acetylornithine deacetylase controls ornithine biosynthesis via a linear pathway with downstream effects on polyamine levels

Arabidopsis thaliana At4g17830 codes for a protein showing sequence similarity with the Escherichia coli N-acetylornithine deacetylase (EcArgE), an enzyme implicated in the linear ornithine (Orn) biosynthetic pathway. In plants, N-acetylornithine deacetylase (NAOD) activity has yet to be demonstrated; however, At4g17830-silenced and mutant (atnaod) plants display an impaired reproductive phenotype and altered foliar levels of Orn and polyamines (PAs). Here, we showed the direct connection between At4g17830 function and Orn biosynthesis, demonstrating biochemically that At4g17830 codes for a NAOD. These results are the first experimental proof that Orn can be produced in Arabidopsis via a linear pathway. In this study, to identify the role of AtNAOD in reproductive organs, we carried out a transcriptomic analysis on atnaod mutant and wild-type flowers. In the atnaod mutant, the most relevant effects were the reduced expression of cysteine-rich peptidecoding genes, known to regulate male\u2013female cross-talk during reproduction, and variation in the expression of genes involved in nitrogen:carbon (N:C) status. The atnaod mutant also exhibited increased levels of sucrose and altered sensitivity to glucose. We hypothesize that AtNAOD participates in Orn and PA homeostasis, contributing to maintain an optimal N:C balance during reproductive development

SNP mapping and identification of QTL for horticultural key breeding traits in eggplant (Solanum melongena L.)

Eggplant genome is relatively unexplored, especially compared to those of the other major Solanaceae crops tomato, pepper and potato. We recently combined the developed Restriction-site Associated DNA (RAD) approach with Illumina DNA sequencing to effect the rapid and mass discovery of both SNP and SSR markers in eggplant for mapping as well as QTL analysis. A subset of 384 SNPs was used to genotype an F2 intraspecific mapping population and integrated into a previously developed genetic linkage map encompassing a total of 415 markers. The framework map includes 12 linkage groups spanning 1,390 cM with an average map distance of 3.8 cM. The newly developed map was used for identifying quantitative trait loci (QTL) for the traits fruit weight, maximum fruit diameter, fruit shape (length max/diameter max) and adaxial leaf lamina anthocyanin in two locations. On the whole 18 and 17 QTLs were identified in both environments, and at least one major QTL for each trait was identified on the basis of both LOD threshold and coefficient of determination (R2) values

Comprehensive Characterization of Simple Sequence Repeats in Eggplant (Solanum melongena L.) Genome and Construction of a Web Resource

We have characterized the simple sequence repeat (SSR) markers of the eggplant (Solanum melongena) using a recent high quality sequence of its whole genome. We found nearly 133,000 perfect SSRs, a density of 125.5 SSRs/Mbp, and also about 178,400 imperfect SSRs. Of the perfect SSRs, 15.6% were complex, with two stretches of repeats separated by an intervening block of &lt;100 nt. Di- and trinucleotide SSRs accounted, respectively, for 43 and 37% of the total. The SSRs were classified according to their number of repeats and overall length, and were assigned to their linkage group. We found 2,449 of the perfect SSRs in 2,086 genes, with an overall density of 18.5 SSRs/Mbp across the gene space; 3,524 imperfect SSRs were present in 2,924 genes at a density of 26.7 SSRs/Mbp. Putative functions were assigned via ontology to genes containing at least one SSR. Using this data we developed an “Eggplant Microsatellite DataBase” (EgMiDB) which permits identification of SSR markers in terms of their location on the genome, type of repeat (perfect vs. imperfect), motif type, sequence, repeat number and genomic/gene context. It also suggests forward and reverse primers. We employed an in silico PCR analysis to validate these SSR markers, using as templates two CDS sets and three assembled transcriptomes obtained from diverse eggplant accessions