This can be explained again by differences in allelic richness of these marker types, with lower assignment success for SNPs, even when the proportional membership threshold was reduced to 0.65.
Multi-allelic markers, mostly microsatellites, had a mean (maximum) of 216 (366) informative meioses, and a mean 3-lod confidence interval of 3.6 cM Bi-allelic markers, including SNP and other marker types, had a mean (maximum) of 55 (191) informative meioses, and were placed within a mean 8.5cMM 3-lod confidence interval.
Allelic richness was not highly correlated between the two marker types (r2 = 0.11).
Our comparison of microsatellite marker types indicate that loci derived from the transcriptome had similar FST but significantly lower allelic richness and expected heterozygosity compared to microsatellites derived from genomic libraries.
Four of the six indicators (excepting allelic size range and M-ratio) that we evaluated can be calculated for any previously popular (e.g., allozymes) or future (e.g., SNPs or genome sequencing) marker types.
Co-dominant markers also provide more complete information in QTL mapping studies [e.g. allowing estimation of additive and dominant allelic effects; [ 38] and are more useful in some genetic analyses, such as estimating population genetic parameters (e.g. inbreeding levels), relative to dominant marker types such as DArT.
In order to test this we performed Welch Two Sample t tests (unpaired, not assuming equal variance, two-tailed) to test for differences between the mean locus specific FST values, expected heterozygosity, and allelic richness of each marker type.
Despite this, a new marker type, named SNP, for Single Nucleotide Polymorphism, is now on the scene and has gained high popularity, even though it is only a bi-allelic type of marker.
MARKER: marker type : clone 1.a.
