American and european tomato history unveiled using haplotype and GBS analyses

Not many historical or archeological records remain from the tomato journey from Solanum pimpinellifolium (SP) to the vintage varieties, however, its domestication, migrations and diversification in Europe can be unveiled using genetic analyses. The study of 628 SP, Solanum lycopersicum var. cerasiforme (SLC), and Solanum lycopersicum var. lycopersicum (SLL) revealed: 1) SP evolved into SLC during a migration from Peru and Ecuador, 2) there is a wild SLC Mesoamerican population, 3) there are no wild SLC populations in Ecuador and Peru, 4) Peruvian and Ecuadorian SLC are an admixture of Mesoamerican SLC and SP, 5) SP introgressions in SLC harbor flowering control and light response genes, 6) at least some Mesoamerican SLL derives from domesticated Peruvian and Ecuadorian SLC. A GBS analysis of 1,254 accessions,Postprint (published version

Unlocking the European traditional tomato genetic resources

The Mediterranean basin countries are considered secondary centres of tomato diversification. However, information on phenotypic and allelic variation of local tomato materials is still limited. To unveil the molecular basis of Southern European tomato phenotypic diversity, we carried out the most comprehensive phenotypic and genomic variability analysis on traditional European tomato by using 1) a collection of 1,499 traditional European tomatoes (TRADITOM collection) and 2) a multipurpose core collection (TCC), comprising 227 European traditional tomato accessions from the original TRADITOM collection, that captured most of genotypic and phenotypic variation and geographical origin present in traditional tomatoPostprint (published version

The first de novo transcriptome of pepino (Solanum muricatum): assembly, comprehensive analysis and comparison with the closely related species S. caripense, potato and tomato

[EN] Background Solanum sect. Basarthrum is phylogenetically very close to potatoes (Solanum sect. Petota) and tomatoes (Solanum sect. Lycopersicon), two groups with great economic importance, and for which Solanum sect. Basarthrum represents a tertiary gene pool for breeding. This section includes the important regional cultigen, the pepino (Solanum muricatum), and several wild species. Among the wild species, S. caripense is prominent due to its major involvement in the origin of pepino and its wide geographical distribution. Despite the value of the pepino as an emerging crop, and the potential for gene transfer from both the pepino and S. caripense to potatoes and tomatoes, there has been virtually no genomic study of these species. Results Using Illumina HiSeq 2000, RNA-Seq was performed with a pool of three tissues (young leaf, flowers in pre-anthesis and mature fruits) from S. muricatum and S. caripense, generating almost 111,000,000 reads among the two species. A high quality de novo transcriptome was assembled from S. muricatum clean reads resulting in 75,832 unigenes with an average length of 704 bp. These unigenes were functionally annotated based on similarity of public databases. We used Blast2GO, to conduct an exhaustive study of the gene ontology, including GO terms, EC numbers and KEGG pathways. Pepino unigenes were compared to both potato and tomato genomes in order to determine their estimated relative position, and to infer gene prediction models. Candidate genes related to traits of interest in other Solanaceae were evaluated by presence or absence and compared with S. caripense transcripts. In addition, by studying five genes, the phylogeny of pepino and five other members of the family, Solanaceae, were studied. The comparison of S. caripense reads against S. muricatum assembled transcripts resulted in thousands of intra- and interspecific nucleotide-level variants. In addition, more than 1000 SSRs were identified in the pepino transcriptome. Conclusions This study represents the first genomic resource for the pepino. We suggest that the data will be useful not only for improvement of the pepino, but also for potato and tomato breeding and gene transfer. The high quality of the transcriptome presented here also facilitates comparative studies in the genus Solanum. The accurate transcript annotation will enable us to figure out the gene function of particular traits of interest. The high number of markers (SSR and nucleotide-level variants) obtained will be useful for breeding programs, as well as studies of synteny, diversity evolution, and phylogeny.Herraiz García, FJ.; Blanca Postigo, JM.; Ziarsolo Areitioaurtena, P.; Gramazio, P.; Plazas Ávila, MDLO.; Anderson, GJ.; Prohens Tomás, J.... (2016). The first de novo transcriptome of pepino (Solanum muricatum): assembly, comprehensive analysis and comparison with the closely related species S. caripense, potato and tomato. BMC Genomics. 17(321). doi:10.1186/s12864-016-2656-817321Anderson GJ, Jansen RK, Kim Y. The origin and relationships of the pepino, Solanum muricatum (Solanaceae): DNA restriction fragment evidence. Econ Bot. 1996;50:369–80.Anderson GJ, Martine CT, Prohens J, Nuez F. Solanum perlongistylum and S. catilliflorum, new endemic Peruvian species of Solanum, Section Basarthrum, are close relatives of the domesticated pepino, S. muricatum. Novon. 2006;16:161–7.Rodríguez-Burruezo A, Prohens J, Fita AM. Breeding strategies for improving the performance and fruit quality of the pepino (Solanum muricatum): A model for the enhancement of underutilized exotic fruits. Food Res Int. 2011;44:1927–35.Yalçin H. Effect of ripening period on composition of pepino (Solanum muricatum) fruit grown in Turkey. 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European traditional tomatoes galore: a result of farmers’ selection of a few diversity-rich loci

A comprehensive collection of 1254 tomato accessions, corresponding to European traditional and modern varieties, early domesticated varieties, and wild relatives, was analyzed by genotyping by sequencing. A continuous genetic gradient between the traditional and modern varieties was observed. European traditional tomatoes displayed very low genetic diversity, with only 298 polymorphic loci (95% threshold) out of 64 943 total variants. European traditional tomatoes could be classified into several genetic groups. Two main clusters consisting of Spanish and Italian accessions showed higher genetic diversity than the remaining varieties, suggesting that these regions might be independent secondary centers of diversity with a different history. Other varieties seem to be the result of a more recent complex pattern of migrations and hybridizations among the European regions. Several polymorphic loci were associated in a genome-wide association study with fruit morphological traits in the European traditional collection. The corresponding alleles were found to contribute to the distinctive phenotypic characteristic of the genetic varietal groups. The few highly polymorphic loci associated with morphological traits in an otherwise a low-diversity population suggests a history of balancing selection, in which tomato farmers likely maintained the morphological variation by inadvertently applying a high selective pressure within different varietal types.This work was supported by the European Commission H2020 research and innovation program through TRADITOM grant agreement no. 634561, G2P-SOL, grant agreement no. 677379, and HARNESSTOM grant agreement no. 101000716. MP is grateful to the Spanish Ministerio de Ciencia e Innovación for a postdoctoral grant (IJC2019-039091-I/AEI/10.13039/501100011033).Postprint (published version

Additional file 9: of The first de novo transcriptome of pepino (Solanum muricatum): assembly, comprehensive analysis and comparison with the closely related species S. caripense, potato and tomato

ClustalW alignment. Text file with multiple alignment from the concatenation of the five genes studied in pepino, tomato, potato, eggplant, pepper and tobacco. (DOCX 34 kb

Transcriptome analysis and molecular marker discovery in Solanum incanum and S. aethiopicum, two close relatives of the common eggplant (Solanum melongena) with interest for breeding

[EN] Background: Solanum incanum is a close wild relative of S. melongena with high contents of bioactive phenolics and drought tolerance. S. aethiopicum is a cultivated African eggplant cross-compatible with S. melongena. Despite their great interest in S. melongena breeding programs, the genomic resources for these species are scarce. Results: RNA-Seq was performed with NGS from pooled RNA of young leaf, floral bud and young fruit tissues, generating more than one hundred millions raw reads per species. The transcriptomes were assembled in 83,905 unigenes for S. incanum and in 87,084 unigenes for S. aethiopicum with an average length of 696 and 722 bp, respectively. The unigenes were structurally and functionally annotated based on comparison with public databases by using bioinformatic tools. The single nucleotide variant calling analysis (SNPs and INDELs) was performed by mapping our S. incanum and S. aethiopicum reads, as well as reads from S. melongena and S. torvum available on NCBI database (National Center for Biotechnology Information), against the eggplant genome. Both intraspecific and interspecific polymorphisms were identified and subsets of molecular markers were created for all species combinations. 36 SNVs were selected for validation in the S. incanum and S. aethiopicum accessions and 96 % were correctly amplified confirming the polymorphisms. In addition, 976 and 1,278 SSRs were identified in S. incanum and S. aethiopicum transcriptomes respectively, and a set of them were validated. Conclusions: This work provides a broad insight into gene sequences and allelic variation in S. incanum and S. aethiopicum. This work is a first step toward better understanding of target genes involved in metabolic pathways relevant for eggplant breeding. The molecular markers detected in this study could be used across all the eggplant genepool, which is of interest for breeding programs as well as to perform marker-trait association and QTL analysis studies.This work has been partially funded by Spanish Ministerio de Economia y Competitividad and FEDER (grant AGL2015-64755-450 R).Gramazio, P.; Blanca Postigo, JM.; Ziarsolo Areitioaurtena, P.; Herraiz García, FJ.; Plazas Ávila, MDLO.; Prohens Tomás, J.; Vilanova Navarro, S. (2016). Transcriptome analysis and molecular marker discovery in Solanum incanum and S. aethiopicum, two close relatives of the common eggplant (Solanum melongena) with interest for breeding. BMC Genomics. 17(300). doi:10.1186/s12864-016-2631-4S1730

Additional file 5: Figure S2. of The first de novo transcriptome of pepino (Solanum muricatum): assembly, comprehensive analysis and comparison with the closely related species S. caripense, potato and tomato

Distribution of GO terms (pdf image). The unigenes distribution regarding the quantity of GO terms to which they are assigned. (PDF 17 kb