An Eggplant Recombinant Inbred Population Allows the Discovery of Metabolic QTLs Controlling Fruit Nutritional Quality

Abstract

Eggplant (Solanum melongena L.) represents the third most important crop of the Solanaceae family and is an important component of our daily diet. A population of 164 F6 recombinant inbred lines (RILs), derived from two eggplant lines differing with respect to several key agronomic traits, “305E40” and “67/3,” was grown to the commercial maturation stage, and fruits were harvested, separated into peel and flesh, and subjected to liquid chromatography Liquid Chromatography/Mass Spectrometry (LC/MS) analysis. Through a combination of untargeted and targeted metabolomics approaches, a number of metabolites belonging to the glycoalkaloid, anthocyanin, and polyamine classes and showing a differential accumulation in the two parental lines and F1 hybrid were identified. Through metabolic profiling of the RILs, we identified several metabolomic quantitative trait loci (mQTLs) associated with the accumulation of those metabolites. Each of the metabolic traits proved to be controlled by one or more quantitative trait loci (QTLs); for most of the traits, one major mQTL (phenotypic variation explained [PVE] ≥ 10%) was identified. Data on mQTL mapping and dominance–recessivity relationships of measured compounds in the parental lines and F1 hybrid, as well as an analysis of the candidate genes underlying the QTLs and of their sequence differences in the two parental lines, suggested a series of candidate genes underlying the traits under study.

A SmelAAT Acyltransferase Variant Causes a Major Difference in Eggplant (Solanum melongena L.) Peel Anthocyanin Composition

“…Genome annotation in combination with sequence differences in the two parental lines supplied a key tool to gather valuable information for QTL fine mapping and for identification of some valuable candidates controlling the synthesis of the considered metabolites. Among them, the gene Smel_005g236240 encoding for a BAHD anthocyanin acyltransferase (hereafter referred to as SmelAAT) was revealed as the most promising candidate for the conversion of D3R into NAS, as the SnpEff analysis performed on the two parental lines revealed a variant that could determine a severe effect in the CDS sequence of the '305E40' parent, in agreement with the biochemical data [32]. In the present work, we used a candidate gene approach to investigate the role of SmelAAT in the differential accumulation of D3R or NAS in lines '305E40' and '67/3', respectively (Figure 1).…”

“…More recently, a RIL population from the intraspecific cross between '305E40' × '67/3' was employed for developing a GBS-based, high-density linkage map and locating QTLs for many fruits traits, including shape and anthocyanin tonality [31]. The same population was recently characterized for the metabolic composition of the fruit peel and flesh, allowing the discovery and location of mQTLs for metabolic compounds belonging to flavonoid, glycoalkaloid, and polyamine classes [32]. In particular, a QTL cluster on E05 was depicted to control, in an opposite way, the levels of D3R and NAS, the two alternative anthocyanin forms characterizing the parental lines of the RIL population.…”

Mutations in the SmAPRR2 transcription factor suppressing chlorophyll pigmentation in the eggplant fruit peel are key drivers of a diversified colour palette

“…In eggplant, this has led to the identification of very few candidate genes controlling traits of interest, lagging it behind other major crops where multiple bi-parental and multi-parent experimental populations have been developed and available for many years already (Gramazio et al, 2018). Luckily, in the last few years, new advanced populations have been developed in eggplant, including recombinant inbred lines (RILs) (Lebeau et al, 2013; Mishra et al, 2020; Toppino et al, 2020; Sulli et al, 2021), and one set of introgression lines (ILs) (Gramazio et al, 2017). These populations have allowed the identification of many and highly relevant QTLs (Mangino et al, 2020; 2021; Toppino et al, 2020; Rosa-Martínez et al, 2022).…”

Genomics and Marker-Assisted Improvement of Vegetable Crops

“…The map, spanning 2169.23 cM, had an average marker distance of 0.4 cM and has been utilized to determine genetic bases of several traits related to anthocyanin content and seed vigor (Toppino et al, 2020). Since the fruit of the two parental lines ("305E40" and "67/3") show different content in several metabolites belonging to the glycoalkaloid, anthocyanin, and polyamine classes, more recently the metabolic profiling of each RIL made it possible the identification of several metabolomic QTLs (mQTLs) associated with their accumulation (Sulli et al, 2021).…”