Construction of a High-Density Recombination Bin-Based Genetic Map Facilitates High-Resolution Mapping of a Major QTL Underlying Anthocyanin Pigmentation in Eggplant

Abstract

High-density genetic maps can significantly improve the resolution of QTL mapping. We constructed a high-density recombination bin-based genetic map of eggplant based on 200 F2 plants from an interspecific cross (Solanum melongena × S. incanum) using the whole genome resequencing strategy. The map was 2022.8 cM long, covering near 99% of the eggplant genome. The map contained 3776 bins, with 3644 (96.5%) being effective (position non-redundant) ones, giving a nominal average distance of 0.54 cM and an effective average distance of 0.56 cM between adjacent bins, respectively. Using this map and 172 F2:3 lines, a major QTL with pleiotropic effects on two anthocyanin pigmentation-related traits, leaf vein color (LVC) and fruit pericarp color (FPC), was steadily detected in a bin interval of 2.28 cM (or 1.68 Mb) on chromosome E10 in two cropping seasons, explaining ~65% and 55% of the phenotypic variation in LVC and FPC, respectively. Genome-wide association analysis in this population validated the QTL and demonstrated the correctness of mapping two bins of chromosome E02 onto E10. Bioinformatics analysis suggested that a WDR protein gene inside the bin interval with reliable effective variation between the two parents could be a possible candidate gene of the QTL.

Genetic and Biotechnological Approaches to Improve Fruit Bioactive Content: A Focus on Eggplant and Tomato Anthocyanins

“…Anthocyanin pigmentation has been a key trait in quantitative trait locus (QTL) studies since the very first molecular linkage maps were developed for eggplant [ 47 , 48 ]. Over the last ten years, a succession of QTL analyses performed with ever-increasing numbers of molecular markers have revealed that regions on two chromosomes are responsible for much of the variation in anthocyanin accumulation in eggplant tissues [ 49 , 50 , 51 , 52 , 53 , 54 , 55 , 56 , 57 , 58 , 59 ].…”

“…The recent availability of an annotated eggplant genome sequence has also allowed researchers to identify candidate genes on eggplant chromosome 10. An amino acid substitution in a WD repeat-containing protein seems to underlie an E10.1 QTL controlling fruit pericarp color [ 57 ]. WD proteins are critical components of the MBW transcription factor complex that regulates anthocyanin biosynthesis.…”

“…In Abg, all five activator genes produce functional TFs; in Aft, the first four are functional, whereas in WT tomato, only the first three activator genes are functional [ 191 ]. There is a high degree of synteny for this locus across the four Solanaceous crops: tomato, eggplant [ 48 , 52 , 61 ], potato [ 229 ], and pepper [ 230 ], and, as described in Section 2.3 , major QTLs underlying the majority of the phenotypic variation in fruit and leaf anthocyanin pigmentation in eggplant were mapped on chromosome 10 [ 48 , 49 , 52 , 54 , 57 ].…”

“…This provides additional support for the importance of chromosome 10 loci in controlling eggplant fruit peel color. The high-density, high-resolution molecular linkage maps recently developed for eggplant [54,57,58] will undoubtedly facilitate marker-assisted selection. And, while early analyses relied on synteny between the chromosomes of eggplant and tomato to associate QTLs with previously identified anthocyanin genes [49,[51][52][53]61], whole genome assemblies and annotations improve the accuracy with which candidate genes underlying anthocyanin accumulation can be predicted.…”

Power Up Plant Genetic Research with Genomic Data

“…In most cases, genetic markers are no longer the limiting factor for genetic mapping; instead, the number of recombination events within the population is the limiting factor. Guan et al resequenced 200 F2 eggplants from an interspecific cross ( Solanum melongena × S. incanum ) for the construction of a recombinant bin map [ 8 ]. Using the phenotypic data of 172 F2:3 lines and this recombinant bin map, a major quantitative trait locus (QTL) was identified corresponding to the leaf vein color and fruit pericarp color.…”