Genomic Tools for the Enhancement of Vegetable Crops: A Case in Eggplant

Abstract

Dramatic advances in genomics during the last decades have led to a revolution in the field of vegetable crops breeding. Some vegetables, like tomato, have served as model crops in the application of genomic tools to plant breeding but other important crops, like eggplant (Solanum melongena), lagged behind. The advent of next generation sequencing (NGS) technologies and the continuous decrease of the sequencing costs have allowed to develop genomic tools with a greatly benefit for no-model plants such as eggplant. In this review we present the currently available genomic resources in eggplant and discuss their interest for breeding. The first draft of eggplant genome sequence and the new upcoming improved assembly, as well as the transcriptomes and RNA-based studies represent important genomic tools. The transcriptomes of cultivated eggplant and several wild relatives of eggplant are also available and have provided relevant information for the development of markers and understanding biological processes in eggplant. In addition, a historical overview of the eggplant genetic mapping studies, performed with different types of markers and experimental populations, provides a picture of the increase over time of the precision and resolution in the identification of candidate genes and QTLs for a wide range of stresses, and morphoagronomic and domestication traits. Finally, we discuss how the development of new genetic and genomic tools in eggplant can pave the way for increasing the efficiency of eggplant breeding for developing improved varieties able to cope with the old and new challenges in horticultural production.

Whole-Genome Resequencing of Seven Eggplant (Solanum melongena) and One Wild Relative (S. incanum) Accessions Provides New Insights and Breeding Tools for Eggplant Enhancement

“…This pioneering resequencing study has significant relevance for eggplant breeding. In this way, these eight accessions are the founders of an eight-way MAGIC population that is currently under development and which may make a significant impact in eggplant breeding (Cavanagh et al, 2008; Gramazio et al, 2018). 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.…”

“…Common eggplant ( Solanum melongena L., 2 n = 2 x = 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). Despite its importance in many tropical and subtropical areas, eggplant has lagged behind other major crops in the development of genetic and genomic tools (Gramazio et al, 2018). However, 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).…”

Heterosis Breeding in Eggplant (Solanum melongena L.): Gains and Provocations

“…Instead of tremendous diversity and beneficial alleles for biotic and abiotic stress present in wild relatives, there has been little progress made on in its overall improvement [33]. One of the significant obstacles to the use of alleles of wild species into cultivated eggplant the is lack of a genome sequence database [34]. However, the recently mapping population developed from several crosses between eggplant and its wild relatives [35].…”

World Vegetable Center Eggplant Collection: Origin, Composition, Seed Dissemination and Utilization in Breeding

“…This information, combined with genomics studies for the detection of genes and QTLs of agronomic importance and their associated markers, will be of great utility in eggplant breeding, as has been demonstrated in some association mapping studies (Cericola et al, 2014 ; Portis et al, 2015 ). Recent reviews of the development in eggplant is provided by Frary and Doganlar ( 2013 ) and Gramazio et al ( in press ).…”