SSRs (Microsatellite markers) are important because of their locus-specific codominant and multiallelic nature, significant abundance in the genome, and high rates of transferability across species (Saha et al. 2006; Aggarwal et al. 2007).
Because of their high polymorphism, microsatellite loci currently represent the most widely used DNA technologies to detect whether losses of genetic diversity have occurred within captive breeding programs.
Genomic data from the pufferfishes Fugu rubripes and Tetraodon nigroviridis were not useful in this analysis because the locations of their Pgi loci were not determined.
CRISPR are consistently described as among the most rapidly evolving genomic loci because of their presumed evolutionary role as an immunity system.
Inbreeding increases the probability that the parents share alleles at pairs of linked loci because of their relatedness and the inbreeding of common ancestors (Hill and Weir 2012).
The spiggin cDNAs (spg1-spg4) are extremely unlikely to contain alleles at spiggin loci because of their sequence diversity (Fig. 3).
Despite these potential caveats, several genomewide studies have identified genes that may be good candidates for selected loci because of their outlier behaviour with respect to the rest of the genome (Carlson et al. 2005; Voight et al. 2006; Frazer et al. 2007; Sabeti et al. 2007; Tang et al. 2007; Barreiro et al. 2008).
Also by means of LAPEA we analysed the full set of 230 AFLP loci and the set of 43 AFLP loci selected because of their high among taxon Fst values.
The genes of milk proteins and hormones are excellent candidate genes for linkage analysis with quantitative trait loci (QTL) because of their biological significance on the quantitative traits of interest.
Rather, control may lie in mutations at a few key loci that, because of their position in a pathway (e.g. branch points [ Eanes 1999]), can affect fitness.
Additionally, this study provides a new example of the identification of rare variants in common-allele-associated loci, which, because of their extremely low frequencies, are not statistically associated.
