Comparison of transcriptome-derived simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers for genetic fingerprinting, diversity evaluation, and establishment of relationships in eggplants

[EN] Simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers are amongst the most common markers of choice for studies of diversity and relationships in horticultural species. We have used 11 SSR and 35 SNP markers derived from transcriptome sequencing projects to fingerprint 48 accessions of a collection of brinjal (Solanum melongena), gboma (S. macrocarpon) and scarlet (S. aethiopicum) eggplant complexes, which also include their respective wild relatives S. incanum, S. dasyphyllum and S. anguivi. All SSR and SNP markers were polymorphic and 34 and 36 different genetic fingerprints were obtained with SSRs and SNPs, respectively. When combining both markers all accessions but two had different genetic profiles. Although on average SSRs were more informative than SNPs, with a higher number of alleles, genotypes and polymorphic information content (PIC), and expected heterozygosity (He) values, SNPs have proved highly informative in our materials. Low observed heterozygosity (Ho) and high fixation index (f) values confirm the high degree of homozygosity of eggplants. Genetic identities within groups of each complex were higher than with groups of other complexes, although differences in the ranks of genetic identity values among groups were observed between SSR and SNP markers. For low and intermediate values of pair-wise SNP genetic distances, a moderate correlation between SSR and SNP genetic distances was observed (r(2) = 0.592), but for high SNP genetic distances the correlation was low (r(2) = 0.080). The differences among markers resulted in different phenogram topologies, with a different eggplant complex being basal (gboma eggplant for SSRs and brinjal eggplant for SNPs) to the two others. Overall the results reveal that both types of markers are complementary for eggplant fingerprinting and that interpretation of relationships among groups may be greatly affected by the type of marker used.This work has been funded by European Union's Horizon 2020 Research and Innovation Programme under Grant Agreement No 677379 (G2P-SOL project: Linking genetic resources, genomes and phenotypes of Solanaceous crops) and by Spanish Ministerio de Economia y Competitividad and Fondo Europeo de Desarrollo Regional (Grant AGL2015-64755-R from MINECO/FEDER). Pietro Gramazio is grateful to Universitat Politecnica de Valencia for a pre-doctoral contract (Programa FPI de la UPV-Subprograma 1/2013 call). Mariola Plazas is grateful to Spanish Ministerio de Economia, Industria y Competitividad for a post-doctoral grant within the Juan de la Cierva-Formacion programme (FJCI-2015-24835).Gramazio, P.; Prohens Tomás, J.; Borras, D.; Plazas Ávila, MDLO.; Herraiz García, FJ.; Vilanova Navarro, S. 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Evaluation of androgenic competence through anther culture in common eggplant and related species

Anther culture is a convenient technique to obtain androgenic haploid and doubled haploid (DH) plants. In common eggplant (Solanum melongena), this technique has been used to develop DH pure lines for producing uniform F1 hybrid seed of some commercial varieties. However, a comprehensive study of the variation of this useful trait among different materials of common eggplant and related species is still lacking. In this work, we studied the androgenic response of 12 accessions of common eggplant and related materials from the primary (eggplant complex) and secondary genepools. We cultured anthers of all the accessions under the same experimental conditions, and studied their competence to produce calli, embryos and plants, as well as the quality and origin of the embryos produced. In our conditions, anthers of 11 out of the 12 accessions produced somatic calli, whereas only 5 also produced microspore-derived embryos, with variable results in terms of embryo quality and of frequency of embryo induction and plant germination. Embryos of responding accessions were initially haploid, and reached the DH status, verified with SSR markers, after a defined period of culture. In addition to other aspects common to many androgenesis-responsive species, our results allowed us to extract conclusions particular to common eggplant and relatives, including the difficulty for finding sources of androgenic competence out of S. melongena, the reduced impact of calli in the production of non-DH individuals, and the need to avoid the occurrence of severe anatomical and functional problems in the apex of most embryos, which seriously reduces their germinative success. © 2011 Springer Science+Business Media B.V.We acknowledge Drs. Begona Renau and Antonio Serrano, and Mrs Nuria Palacios for their excellent technical work, as well as the staff of the COMAV greenhouses for their valuable help. Thanks are also due to Dr. Santiago Vilanova for providing us with the SSRs used in this work. This work was supported by grants from Spanish MICINN AGL2006-06678 and AGL2010-17895 to JMSS, and AGL2009-07257 to JP.Salas Aragon, P.; Prohens Tomás, J.; Seguí-Simarro, JM. (2011). Evaluation of androgenic competence through anther culture in common eggplant and related species. Euphytica. 182(2):261-274. doi:10.1007/s10681-011-0490-2S261274182

Characterization of interspecific hybrids and backcross generations from crosses between twocultivated eggplants (Solanum melongena and S. aethiopicum Kumba group) and implications for eggplant breeding

Common (Solanum melongena L.) and scarlet (S. aethiopicum L.) eggplants are cultivated for their fruits and form part of the same genepool. We have studied plant and fruit characteristics, pollen viability and seed set, phenolics content, and fruit flesh browning in accessions of S. melongena and S. aethiopicum Kumba group, as well as interspecific hybrids between these species and first backcross generations to each parental species. Respective genotypes were also characterized with seven polymorphic SSR markers. The results demonstrate that many differences exist for plant and fruit morphology among S. melongena, S. aethiopicum and the interspecific hybrids. The latter are very vigorous and generally intermediate between the two parents, except for fruit size which is smaller (and parthenocarpic due to a high pollen sterility) than those of any of the parents. Backcross progenies also exhibited morphological variation with moderate heritability values for the attributes evaluated. Variation for fruit size was present in the backcross generations but fruits were small resulting in little variation for fruit shape. Backcross plants with moderate fertility produced seeded fruits. Primary hybrids had fruit phenolics content similar to that of S. aethiopicum, the parent with lowest phenolics concentration, and were heterotic for fruit flesh browning. Backcross progenies were quite variable for both traits. SSR markers did not reveal segregation distortion in the backcross generations for these interspecific hybrids. The results demonstrate that generations derived from sexual interspecific hybridization can be a powerful tool for S. melongena and S. aethiopicum Kumba group breeding. © 2012 Springer Science+Business Media B.V.This work was partially financed by the Ministerio de Ciencia y Tecnologia (AGL2009-07257 and RF-2008-00008-00-00).Prohens Tomás, J.; Plazas Ávila, MDLO.; Raigón Jiménez, MD.; Seguí-Simarro, JM.; Stommel, JR.; Vilanova Navarro, S. (2012). Characterization of interspecific hybrids and backcross generations from crosses between twocultivated eggplants (Solanum melongena and S. aethiopicum Kumba group) and implications for eggplant breeding. Euphytica. 186(2):517-538. doi:10.1007/s10681-012-0652-xS517538186