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 F2 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.

QTL hotspots in eggplant (Solanum melongena) detected with a high resolution map and CIM analysis

“…As a master switch that upregulates nearby genes involved in anthocyanin biosynthesis (CHS) and modification (3GT) (Mathews et al 2003), ANT1 could be an especially valuable target for improving eggplant peel color. While another major cluster of anthocyanin QTL was localized on chromosome 5 in the Barchi et al (2012) intraspecific population, corolla anthocyanin (ca5.1) is the only trait that maps in this region in the current study. A single candidate gene resides in this region of the tomato genome, 5GT (encoding 5-Oglucosyltransferase) (Barchi et al 2012).…”

“…While another major cluster of anthocyanin QTL was localized on chromosome 5 in the Barchi et al (2012) intraspecific population, corolla anthocyanin (ca5.1) is the only trait that maps in this region in the current study. A single candidate gene resides in this region of the tomato genome, 5GT (encoding 5-Oglucosyltransferase) (Barchi et al 2012). Of the other pigment QTL detected in the two studies, the only other overlap was seen on chromosome 11, between loci for abaxial leaf lamina anthocyanin (ablanE11.ML; Barchi et al 2012) and fruit anthocyanin intensity (fai11.1).…”

“…In this same vicinity, Barchi et al (2012) found a cluster of QTL controlling anthocyanin levels in six plant parts (stem, leaf lamina, leaf veins, corolla, calyx, peduncle) in their intraspecific S. melongena mapping population. Not surprisingly, several structural and regulatory genes involved in anthocyanin synthesis map to orthologous regions of the tomato genome.…”

“…A single candidate gene resides in this region of the tomato genome, 5GT (encoding 5-Oglucosyltransferase) (Barchi et al 2012). Of the other pigment QTL detected in the two studies, the only other overlap was seen on chromosome 11, between loci for abaxial leaf lamina anthocyanin (ablanE11.ML; Barchi et al 2012) and fruit anthocyanin intensity (fai11.1).…”

“…The addition of nearly 100 AFLP Ò markers to the map allowed the detection of QTL for several other traits (fruit, stem, and calyx color) (Nunome et al 2001). More recently, Barchi et al (2012) developed a linkage map for their intraspecific F 2 population derived from a cross between two breeding lines, '305E40' and '67/3'. The map included over 400 restriction fragment length polymorphism (RFLP) and single nucleotide polymorphism (SNP) markers and enabled the localization of QTL influencing seven pigmentation traits on eight of eggplant's twelve chromosomes.…”