A RAD tag derived marker based eggplant linkage map and the location of QTLs determining anthocyanin pigmentation

Abstract

Both inter- and intra-specific maps have been developed in eggplant (Solanum melongena L.). The former benefit from an enhanced frequency of marker polymorphism, but their relevance to marker-assisted crop breeding is limited. Combining the restriction-site associated DNA strategy with high throughput sequencing has facilitated the discovery of a large number of functional single nucleotide polymorphism (SNP) markers discriminating between the two eggplant mapping population parental lines '305E40' and '67/3'. A set of 347 de novo SNPs, together with 84 anchoring markers, were applied to the F(2) mapping population bred from the cross '305E40' x '67/3' to construct a linkage map. In all, 415 of the 431 markers were assembled into twelve major and one minor linkage group, spanning 1,390 cM, and the inclusion of established markers allowed each linkage group to be assigned to one of the 12 eggplant chromosomes. The map was then used to discover the genetic basis of seven traits associated with anthocyanin content. Each of the traits proved to be controlled by between one and six quantitative trait loci (QTL), of which at least one was a major QTL. Exploitation of syntenic relationships between the eggplant and tomato genomes facilitated the identification of potential candidate genes for the eggplant QTLs related to anthocyanin accumulation. The intra-specific linkage map should have utility for elucidating the genetic basis of other phenotypic traits in eggplant.

Figure 1. Linkage map of eggplant and graphical representation of the QTLs detected.

A) chromosomes E01 to E06; B) chromosomes E07 to E12. Marker names are shown to the right of each chromosome, with map distances (in cM) shown on the left. Map positions of the QTL identified on each chromosome (or LG) are also given on the right. The length of the vertical bars represents the confidence interval of the QTL (LODmax-1 interval). QTL shown in blue were detected only at ML, and those in red only at MT.

Figure 2. Synteny between eggplant chromosomes E5 and E10 and tomato chromosomes segments T5, T10 and T12.

The physical location of the tomato genes encoding chalcone synthase (CHS), UDP-glucose anthocyanidin 3-0 glucosyltansferase (3GT), UDP-glucose anthocyanidin 5-0 glucosyltansferase (5GT) and the transcription factors an2 and ant1 is underlined. QTLs involved in anthocyanin pigmentation in eggplant are also shown. Distances on the eggplant chromosomes are given in cM, and on the tomato chromosome segments in Mbp.