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

Pietro Gramazio,Francisco J Herraiz,Mariola Plazas,Edgar García-Fortea,Santiago Vilanova,Jaime Prohens,Giulio Mangino

doi:10.15835/nbha46110936

Pietro Gramazio, Francisco J Herraiz + Show 5 more

Open Access

https://doi.org/10.15835/nbha46110936

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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 morpho-agronomic 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.

Highlights

Eggplant (Solanum melongena L., 2n = 2x = 24), known as common eggplant or brinjal eggplant, belongs to the Leptostemonum clade within the Solanum genus and is the second most important solanaceous fruit crop in total production after tomato (S. lycopersicum L.) (Knapp et al, 2013)
In this review we present the currently available genomic resources in eggplant and discuss their interest for breeding
Eggplant has undergone a constant increase in yield (2.7-fold) and total production (8.7-fold) in the last fifty years, the largest increases have been recorded in the last decade (FAOSTAT, 2017)

Summary

Introduction

A large number of different simple sequence repeats (SSRs) motifs and repeats (83,401) was identified by Hirakawa et al (2014), as well as 4,536 single nucleotide polymorphisms (SNPs) from a microarray among the accessions used for the study This first genomic resource, which is quite far to be a comprehensive work, paved the way to understanding the genomic architecture of the eggplant and allowed to perform comparisons with other important Solanaceae crops, like potato, tomato and pepper (Potato Genome Sequencing Consortium, 2011; The Tomato Genome Consortium, 2012; Qin et al, 2014), whose genomes are more complete and annotated, and with model species like Arabidopsis thaliana (Cheng et al, 2016). From paired-end 2x100 bp libraries, these authors retrieved 15 M of raw reads, which were assembled after a filtering process in 44,672 transcripts and 34,174 unigenes, a similar number to the

Aim of the study

Findings

28 SSRs 1 SRAP