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The selection of the loci set was based on their polymorphism and unambiguously sized PCR product.
Five microsatellite loci were chosen based on their polymorphism information, ease of scoring, and reproducibility (Table 1).
Microsatellite markers (Table S2) were selected based on their polymorphism and map information (Loridon et al. 2005) to build the framework maps of the three new populations.
We selected 17 loci among the developed SSR markers [ 22- 25] based on their polymorphism and ease of scoring following the screening of 16 distinct Mediterranean varieties.
The proportion of monomorphic markers was almost zero for SNP and SSR probably because most of SSR and SNP markers were selected based on their polymorphism among a set of 5-8 genotypes [ 12, 46].
cDNA-amplified fragment length polymorphism (cDNA-AFLP), which does not require prior sequence information, is an efficient, sensitive, and reproducible technology for the discovery and identification of genes based on their polymorphism or differential expression patterns [ 32].
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MHC class I genes can be further grouped as either classical (class Ia) or nonclassical (class Ib) based on their polymorphisms, expression levels, and functions [ 13].
These 34 markers were selected based on their high polymorphism rate of at least three alleles in the 12 potential parents.
The phylogenetic analysis of SSR locus 8 partial sequences was even more informative and separated the isolates into 8 genotypes based on their nucleotide polymorphisms.
The following ten microsatellite loci, developed specifically for raccoons, were selected based on their size and polymorphism (see Table S1 for details about loci): PLO-M2, PLO-M3, PLO-M15, PLO-M17, PLO-M20, PLO2-14, PLM06117, PLM10, PLM10 and PLM20 (Cullingham et al. 2006; Siripunkaw et al. 2008).
Phylogenetic analysis of SSR locus 8 sequences based on their single nucleotide polymorphisms separated the isolates into 8 genotypes.
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