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

Date Published: July 7, 2017

Publisher: Public Library of Science

Author(s): Alberto Acquadro, Lorenzo Barchi, Pietro Gramazio, Ezio Portis, Santiago Vilanova, Cinzia Comino, Mariola Plazas, Jaime Prohens, Sergio Lanteri, Mohar Singh.

http://doi.org/10.1371/journal.pone.0180774

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.

Partial Text

Eggplant, also known as brinjal eggplant or aubergine (Solanum melongena L., Solanaceae, 2n = 2x = 24), is cultivated worldwide and is one of the most important vegetable crops, being the second most important solanaceous crop grown for its fruit after tomato (S. lycopersicum L.) [1]. The bulk of eggplant production is concentrated in China, India, Iran, Egypt and Turkey, with Italy and Spain representing the most important European Union producers [1]. Because of its importance as a staple vegetable food in many countries from tropical and subtropical regions, eggplant is included with 34 other food crops in the Annex 1 of the International Treaty on Plant Genetic Resources for Food and Agriculture [2]. Eggplant berries are a source of dietary minerals as well as vitamins and other health-promoting metabolites such as anthocyanins and chlorogenic acid, with nutraceutical and anti-oxidant properties [3–6].

One of the most exciting developments in the past decade has been the application of powerful and ultra-rapid nucleic acid sequencing techniques to the study of genetic relationships and phylogeny of crop species [78]. As previously reported by Bajaj et al. [79] in chickpea, our results demonstrate that the high-throughput genotyping of numerous genome-wide SNP markers represents a highly and more effective approach, in respect to the ones based on limited sets of genome-wide markers or a small set of gene sequences, for understanding the extent of natural allelic diversity and genetic relationships among and within wild and cultivated species belonging to eggplant complexes. The high number of detected polymorphisms were analysed by FastSTRUCTURE [48, 49], UPGMA and PCoA analyses and the three approaches showed to be complementary in the interpretation of data. On the whole, we confirm a wide genetic base and broad molecular diversity among wild and cultivated species within and among the three cultivated eggplant complexes and the New World eggplant CWRs. Thanks to a reduced complexity genome sequencing approach, we were able to fingerprint all accessions in the study and gathered information which may efficiently guide further exploration of the diversity and relationships in the large Solanum subgenus Leptostemonum group. The approach used and data obtained lay the foundation also to address the evaluation of gene flow among inter-fertile sympatric taxa [71], recent speciation and domestication processes of cultivated eggplants. In addition, the large number of markers distributed across the genome may also contribute to facilitate the transfer of target genomic regions controlling useful agronomic traits, such as biotic and abiotic stress tolerance or fruit quality traits, from related species into the genetic background of cultivated eggplants.

 

Source:

http://doi.org/10.1371/journal.pone.0180774

 

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