In an ultra-saturated genetic map of pepper, contigs that are spanning a QTL can be further examined for their role in one or more metabolic pathways.
We have also leveraged the information to develop an Affymetrix tiling array to construct two ultra-saturated genetic maps of pepper [ 27] and to evaluate genetic diversity in pepper breeding germplasm [ 11].
Alignment of maps with the tomato and potato genomes shows the presence of previously known translocations and a translocation event that was not observed in previous genetic maps of pepper.
However, due to their nature, the majority of these markers, except COSII and tomato cDNA markers, that have been used in the published genetic maps of pepper are not high throughput or gene-based.
The haploid chromosome number for Capsicum is 12; however, when details have been reported for construction of pepper maps, de novo clustering of markers into 12 linkage groups has been rare, with upwards of 20 linkage groups being identified (Prince et al. 1993; Livingstone et al. 1999; Chaim et al. 2001; Lefebvre et al. 2002; Sugita et al. 2005; Barchi et al. 2007; Truong et al. 2010).
We developed two ultradense genetic linkage maps for pepper from single-position polymorphisms (SPPs) identified de novo with a 30,173 unigene pepper genotyping array.
We analyzed synteny between each pepper map and the assembled genomes of pepper's close solanaceous relatives, tomato and potato (File S5, Table S13, Table S14, Table S15, Table S16, and Figure 9).
In this paper, we describe the genetic mapping of these unigenes in one interspecific and one intraspecific mapping population, relating it to the draft genome sequence of pepper, and show synteny with other Solanaceae crop genomes.
Overall, we were able to map >17,500 unigenes representing over 3,000 genetic bins of pepper [ 27].
Various types of molecular marker have been used to conduct phylogenetic and mapping studies in pepper (Capsicum annuum), among which microsatellites (SSRs) have been shown to be particularly valuable because of their co-dominant and multi-allelic nature.
