For 22 positive WBC with three positive QC-PCRs, we then tested the allelic discovery rate on few microsatellite and polymorphic loci amenable for restriction length polymorphism analysis (five single nucleotide polymorphisms and five microsatellite repeat polymorphisms).
Illustrated below are some examples of microsatellites and their polymorphic effects on the coding regions.
To examine the relative value of markers within this group, Amar et al. (2011) compared SRAP, SSR (or microsatellites), and cleaved amplified polymorphic sequences from single nucleotide polymorphic (CAPS-SNP) markers in a Citrus germplasm collection.
In this work, we identified a large number of microsatellites from BAC end sequences of channel catfish, characterized the microsatellites, tested their utility for linkage mapping in a resource family used for genetic mapping, and constructed a web-searchable database for BAC end sequences, their linked microsatellites, microsatellite primers, PCR conditions, and polymorphic information.
Both the (AT 16 24 microsatellite and the polymorphic GalileoN insertion were excluded from the analysis.
We identified 2 polymorphic microsatellites and 33 single nucleotide polymorphisms from a group of 13 individuals and CHORI-241 BAC 100I10 (Table 2).
Variation in the distribution of repeat motifs associated with monomorphic and polymorphic microsatellites was also found.
Polymorphism comparison of the di-nucleotide and tri-nucleotide markers showed that they had similar average PIC values (0.131 and 0.125, respectively) when considering both monomorphic and polymorphic microsatellites together.
In fact, previously we could not identify linkage with T2D at 12q24 using multiple highly informative and polymorphic microsatellites within the same family dataset (data not shown) in which the linkage was identified using SNPs [ 13].
Genotyping of the microsatellites using genomic DNA from sea bream caught at different geographic locations and a family panel, revealed both microsatellites are polymorphic and the locus sbPAC1B scores more alleles (8 alleles) than sbPAC1A (4 alleles) (Additional file 1).
