QTL analysis of morphological traits in eggplant and implications for conservation of gene function during evolution of solanaceous species

Abstract

An interspecific F 2 population from a cross between cultivated eggplant, Solanum melongena, and its wild relative, S. linnaeanum, was analyzed for quantitative trait loci (QTL) affecting leaf, flower, fruit and plant traits. A total of 58 plants were genotyped for 207 restriction fragment length polymorphism (RFLP) markers and phenotyped for 18 characters. One to eight loci were detected for each trait with a total of 63 QTL identified. Overall, 46% of the QTL had allelic effects that were the reverse of those predicted from the parental phenotypes. Wild alleles that were agronomically superior to the cultivated alleles were identified for 42% of the QTL identified for flowering time, flower and fruit number, fruit set, calyx size and fruit glossiness. Comparison of the map positions of eggplant loci with those for similar traits in tomato, potato and pepper revealed that 12 of the QTL have putative orthologs in at least one of these other species and that putative orthology was most often observed between eggplant and tomato. Traits showing potential orthology were: leaf length, shape and lobing; days to flowering; number of flowers per inflorescence; plant height and apex, leaf and stem hairiness. The functionally conserved loci included a major leaf lobing QTL (llob6.1) that is putatively orthologous to the potato leaf (c) and/or Petroselinum (Pts) mutants of tomato, two flowering time QTL (dtf1.1, dtf2.1) that also have putative counterparts in tomato and four QTL for trichomes that have potential orthologs in tomato and potato. These results support the mounting evidence of conservation of gene function during the evolution of eggplant and its relatives from their last common ancestor and indicate that this conservation was not limited to domestication traits.

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

“…The map locations of the 49 remaining QTL corresponded fairly closely to those of QTL detected by Doganlar et al (2002b) and Frary et al (2003a) using simple linear regression analysis. The peak position of each of these QTL shifted an average of ±6.8 cM as compared to the map position of its previously identified counterpart.…”

“…In a previous analysis of this interspecific eggplant population, simple linear regression analysis found 123 significant (P B 0.01) QTL for the 40 morphological traits (Doganlar et al 2002b;Frary et al 2003a). Over half of those loci (54 %) were not detected in this follow-up study using CIM, with more stringent individual trait LOD thresholds (P B 0.01) (determined empirically from 1,000 permutations of the data) to reduce the incidence of false positives.…”

“…Trait means, and gene actions (d/a) were determined for each significant QTL using the CIM results. QTL detected in the present study were compared to those identified in the previous two studies conducted in this population (Doganlar et al 2002b;Frary et al 2003a). Because these QTL were localized on a lower resolution version of the interspecific eggplant map (Doganlar et al 2002a), the map positions and relative lengths of these previously identified QTL on the current molecular map (Doganlar et al in press) were determined using shared RFLP markers as anchors.…”

“…Because S. linnaeanum is a prickly wild relative of eggplant that produces small, round, green, striped fruit while MM738 is a non-spiny commercial cultivar that produces large, oblong, purple fruit without striping, the F 2 population derived from these parents was highly polymorphic. Twenty-two domestication traits (fruit size, shape and color and plant prickliness) (Doganlar et al 2002b) and 18 morphological traits (leaf, flower and fruit size, shape, appearance, and development) (Frary et al 2003a) were evaluated in the population and subjected to single-point linear regression analysis. A total of 125 significant QTL were positioned on the interspecific map.…”

High resolution map of eggplant (Solanum melongena) reveals extensive chromosome rearrangement in domesticated members of the Solanaceae

“…The first interspecific map S. linnaeanum 'MM195' 9 S. melongena 'MM738' (Doganlar et al 2002a) took advantage of the close relationship between eggplant and tomato; 233 tomato restriction fragment length polymorphism (RFLP) markers were positioned in the eggplant genome, allowing for the first comparisons of genome evolution in eggplant, tomato and potato. Moreover, this map provided the foundation for the first quantitative trait mapping analyses in the crop (Doganlar et al 2002b, Frary et al 2003. Sunseri et al (2003), using S. linnaeanum 9 S. melongena 'Buia', described a combined RAPD and AFLP marker map and reported preliminary mapping of Verticillium wilt resistance QTL in their interspecific F 2 population.…”