Abstract
Whole-genome resequencing provides information of great relevance for crop genetics, evolution, and breeding. Here, we present the first whole-genome resequencing study using seven eggplant (Solanum melongena) and one wild relative (Solanum incanum) accessions. These eight accessions were selected for displaying a high phenotypic and genetic diversity and for being the founder parents of an eggplant multiparent advanced generation intercrosses population. By resequencing at an average depth of 19.8× and comparing to the high-quality reference genome “67/3” over 10 million high-reliable polymorphisms were discovered, of which over 9 million (84.5%) were single nucleotide polymorphisms and more than 700,000 (6.5%) InDels. However, while for the S. melongena accessions, the variants identified ranged from 0.8 to 1.3 million, over 9 million were detected for the wild S. incanum. This confirms the narrow genetic diversity of the domesticated eggplant and suggests that introgression breeding using wild relatives can efficiently contribute to broadening the genetic basis of this crop. Differences were observed among accessions for the enrichment in genes regulating important biological processes. By analyzing the distribution of the variants, we identified the potential footprints of old introgressions from wild relatives that can help to unravel the unclear domestication and breeding history. The comprehensive annotation of these eight genomes and the information provided in this study represents a landmark in eggplant genomics and allows the development of tools for eggplant genetics and breeding.
Highlights
Common eggplant (Solanum melongena L., 2n = 2x = 24) is the fifth economically most important vegetable crop, and in the last few years, it has undergone a remarkable increase in yield and total production (Faostat, 2017)
The aim of this study was to interrogate the entire genome of these accessions to provide a large set of robust and high-confidence molecular markers in a very diverse eggplant germplasm set for breeding purposes, genetic and genomic studies, and to develop a highthroughput genotyping platform to efficiently assist the future characterization of the multiparent advanced generation intercrosses (MAGIC) population under development
Pascual et al (2015) emphasized the importance of the information generated by the resequencing of the founder parents of a tomato MAGIC population in the mapping precision of quantitative trait loci, even if many tools and molecular markers were already available in this crop
Summary
Recent efforts have been done to close the gap between eggplant and other model species where more genomic information is available (Yang et al, 2014; Gramazio et al, 2016; Zhou et al, 2016) In this way, the significant improvements in next-generation sequencing (NGS) technologies and the associated substantial cost reductions have fostered genomic studies for crops like eggplant. The significant improvements in next-generation sequencing (NGS) technologies and the associated substantial cost reductions have fostered genomic studies for crops like eggplant In this respect, the release of reference whole-genome sequences represents an important landmark for undertaking other genomic studies, as it has occurred for the most economically important cultivated crops (Weigel and Mott, 2009; Xu et al, 2012; Aflitos et al, 2014; Zhou et al, 2015; Du et al, 2018). The wholegenome resequencing approach is a powerful breeding tool that can foster the development of a new generation of resilient varieties adapted to present and future challenges like climate change
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