Coding SNPs analysis highlights genetic relationships and evolution pattern in eggplant complexes

Abstract

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.

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. 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. 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

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).