As suggested by Carter et al. [ 92], association analyses were also performed between the phenotypic data and a set of reduced haplotypes (minihaplotypes, MH), which were inferred as previously detailed but considering only the most informative polymorphisms.
The 191 SxG offsprings have been previously genotyped for 97 SSR markers to cover the genome with minimal inter-marker space (maximum of 10 cM) with the most informative polymorphisms (priority given to 1 1 1 1 segregating markers).
Based on pairwise linkage disequilibrium, haplotype block structures, and structure of genes, we identified the 14 most informative single nucleotide polymorphisms in the region (Table 2).
The most informative TagSNP and polymorphisms located in the putative transcription factor binding sites were identified using S NPinfo (http://www.snpinfo.niehs.nih.gov).nih.gov
A set of 11 multiplex panels for the simultaneous amplification of the 30 most informative markers (ranked by their Polymorphism Information Content) is made available.
In order to select the most informative combinations (those with a higher level of polymorphism) different combinations were tested using template DNA from the parental lines and 9 offspring.
Therefore MIPs were selected using available polymorphism data to identify diagnostic markers most informative for the mapping purposes.
Compared with conventional molecular markers, such as RFLPs, SSRs or single nucleotide polymorphism markers, bin markers are the most informative and parsimonious set for a given population [ 28].
The IVT data (IVT) are perhaps the most informative control dataset, because rather than modeling errors, alignment, polymorphisms, base representation, it simply has them as they occur naturally yet we still know the ground truth in terms of what the true transcript models are.
Thanks David, most informative.
