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Second, the markers can serve as a rigid interface between a BAC-based physical map with genetic maps.
First, we performed parametric and non-parametric genome-wide linkage analyses using a dense SNP-marker map with genetic data filtered for genotypes mapping to CNVs.
The abundance of markers and accuracy of localization using SNPs associated with BAC-end sequences will be extremely helpful for integrating an allotetraploid cotton physical map with genetic maps.
An example of integration of the genetic and physical map with genetic markers for a detailed region of ~8 cM length on linkage group (LG) is illustrated in Figure 3.
The integration of physical map with genetic maps has been reported earlier in different model plant species including Arabidopsis (Meinke et al. 2009), rice (Chen et al. 2002) and fruit trees including peach (Zhebentyayeva et al. 2008), papaya (Yu et al. 2009) and apple (Han et al. 2011).
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BAC-derived markers can be used to integrate physical maps with genetic maps [ 36, 43], and also facilitate map-based cloning [ 44, 45].
Bedford et al. have now developed an approach to combine antigenic maps with genetic information about the four subtypes of the human flu virus.
Keeping in view the importance of integrating physical maps with genetic maps, we tried to anchor our physical map assembly with the genetic map by fingerprinting of 337 BAC clones and assembly of 319 of these clones into physical map assembly.
Exchange of DNA and genotype data of the T × E bin set in the peach research community is helping candidate gene mapping, with genetic analysis and breeding applications following on.
In this report, the alignment of two genetic maps was successfully performed to assign the linkage groups of the new genetic map with previous genetic maps.
To our knowledge, this is also the highest percentage of physical maps integration with genetic maps that were obtained in any aquaculture species.
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