The identification of large numbers of SNPs for crops would allow the generation of dense linkage maps enabling applications such as high resolution QTL analysis, fine-mapping and map-based gene cloning [ 17, 18].
Dense consensus genetic maps based on high-throughput genotyping platforms are valuable for making genetic gains in Brassica napus through quantitative trait locus identification, efficient predictive molecular breeding, and map-based gene cloning.
Due to the lack of polymorphism at the DNA level, the crop has not been subject to marker-assisted breeding and map-based gene cloning, however, this status is being ameliorated following the development of polymorphic markers (Macedo et al. 2012).
Molecular markers are useful tools for genetic research and breeding, including genotype fingerprinting, genetic diversity analysis, phylogenetic analysis, map-based gene cloning, variety identification and marker-assisted breeding (McCouch et al. 1997; Joshi et al. 2001; Nagaraju et al. 2002; Ni et al. 2002).
Alignment of this physical map with a genetic map of Brachypodium [15] identified long-range collinearity between the physical and genetic maps, thereby supporting the physical map assemblies and providing a useful resource for map-based gene isolation by aligning BACs with genetic markers and recombination data.
The construction of whole-genome physical map could facilitate genome sequence assembly and map-based gene identification [ 25, 40].
Moreover, SRAP is an effective method for map-based gene cloning and molecular marker assisted selection (MAS).
High-density genetic maps play an important role in fine mapping and map-based gene cloning [ 16, 25, 28].
Moreover, the ultradense genetic map is very powerful in molecular marker development, QTL analysis and map-based gene cloning.
However, the information is still insufficient for map-based gene cloning for cucumber yield and fruit quality improvement.
