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. 2017 Jul 7;12(7):e0180774.
doi: 10.1371/journal.pone.0180774. eCollection 2017.

Coding SNPs Analysis Highlights Genetic Relationships and Evolution Pattern in Eggplant Complexes

Free PMC article

Coding SNPs Analysis Highlights Genetic Relationships and Evolution Pattern in Eggplant Complexes

Alberto Acquadro et al. PLoS One. .
Free PMC article


Brinjal (Solanum melongena), scarlet (S. aethiopicum) and gboma (S. macrocarpon) eggplants are three Old World domesticates. The genomic DNA of a collection of accessions belonging to the three cultivated species, along with a representation of various wild relatives, was characterized for the presence of single nucleotide polymorphisms (SNPs) using a genotype-by-sequencing approach. A total of 210 million useful reads were produced and were successfully aligned to the reference eggplant genome sequence. Out of the 75,399 polymorphic sites identified among the 76 entries in study, 12,859 were associated with coding sequence. A genetic relationships analysis, supported by the output of the FastSTRUCTURE software, identified four major sub-groups as present in the germplasm panel. The first of these clustered S. aethiopicum with its wild ancestor S. anguivi; the second, S. melongena, its wild progenitor S. insanum, and its relatives S. incanum, S. lichtensteinii and S. linneanum; the third, S. macrocarpon and its wild ancestor S. dasyphyllum; and the fourth, the New World species S. sisymbriifolium, S. torvum and S. elaeagnifolium. By applying a hierarchical FastSTRUCTURE analysis on partitioned data, it was also possible to resolve the ambiguous membership of the accessions of S. campylacanthum, S. violaceum, S. lidii, S. vespertilio and S. tomentsum, as well as to genetically differentiate the three species of New World Origin. A principal coordinates analysis performed both on the entire germplasm panel and also separately on the entries belonging to sub-groups revealed a clear separation among species, although not between each of the domesticates and their respective wild ancestors. There was no clear differentiation between either distinct cultivar groups or different geographical provenance. Adopting various approaches to analyze SNP variation provided support for interpretation of results. The genotyping-by-sequencing approach showed to be highly efficient for both quantifying genetic diversity and establishing genetic relationships among and within cultivated eggplants and their wild relatives. The relevance of these results to the evolution of eggplants, as well as to their genetic improvement, is discussed.

Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.


Fig 1
Fig 1
SNP numbers and distribution: A) Plot of the number of SNPs (total, homozygous and heterozygous) and missing sites observed within the collection of 76 Solanum accessions; B) The distribution of missing sites along two eggplant chromosomes (i.e.: chr4 and chr8). The trend lines track missing sites in three Solanum melongena and six accessions of American origin (S. elaeagnifolium, S. sisymbriifolium and S. torvum).
Fig 2
Fig 2. The genetic architecture of the full germplasm panel: Consensus UPGMA dendrogram and FastSTRUCTURE output at K = 4.
Bootstrap values (%) for the main nodes are reported in red. Each entry is represented by a vertical line representing sub-group 1 (blue) sub-group 2 (orange), sub-group 3 (yellow) and sub-group 4 (grey). The box reports the Probabilities (p) plots derived from the FastSTRUCTURE analysis of genotypic data with K values from 1 to 9.
Fig 3
Fig 3. The genetic architecture of the full germplasm panel of 76 Solanum accessions.
PCoA visualization of the genetic relationships within the full set of accessions.
Fig 4
Fig 4
Within-groups PCoA analyses in subgroups of germplasm panel of Solanum accessions: visualization of the genetic relationships within sub-group 1 (A; scarlet eggplant complex), sub-group 2 (B; brinjal eggplant complex) and sub-group 4 (C; New World species).

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Grant support

This work has been funded in part 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 Economía, Industria y Competitividad and Fondo Europeo de Desarrollo Regional (grant AGL2015-64755-R from MINECO/FEDER). Funding has also been received from the initiative "Adapting Agriculture to Climate Change: Collecting, Protecting and Preparing Crop Wild Relatives", which is supported by the Government of Norway. This last project is managed by the Global Crop Diversity Trust with the Millennium Seed Bank of the Royal Botanic Gardens, Kew and implemented in partnership with national and international gene banks and plant breeding institutes around the world. For further information see the project website: Pietro Gramazio is grateful to Universitat Politècnica de València for a pre-doctoral (Programa FPI de la UPV-Subprograma 1/2013 call) contract. Mariola Plazas is grateful to Spanish Ministerio de Economía, Industria y Competitividad for a post-doctoral grant within the Santiago Grisolía Programme (FCJI-2015-24835). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.