The multiplex was designed to reduce the amplicon size of the loci found in the AmpFlSTR® SGM Plus® kit.
The kit contains: all 12 loci in the current PowerPlex Y System, the additional 5 loci found in AmpFlSTR Y-filer, plus 6 new loci.
Conversely, all the SD loci found in F2 populations exhibited SD in BC1F1 populations, suggesting that the cause of SD loci in F2 populations can be explained by female and/or male function and/or zygotic selection.
The chromosomal regions of substantial SD loci found in this study were compared to the regions with quantitative trait loci (QTLs) underlying hybrid sterility/fertility and gametophyte genes reported in previous studies on rice.
An analogous study using microsatellite loci found a pattern similar to that in Fig. 5a, with a single domestication origin and some apparent gene flow between the two subspecies of O. sativa (Gao and Innan 2008).
The multiplex was designed to incorporate these five new loci as mini- and midi-STRs while maintaining the loci found in the AmpFlSTR® SGM Plus® kit as standard size.
Pairwise LD was calculated between all of the 2991 loci from unique regions, with 9004 pairs of SNP loci found to be in moderate LD, which is significantly more than the 2078 expected by chance (established by permutation testing).
In such cases, little if any mapping is required since the phenotype-causing mutant locus will be one of the few, if not only loci found to be mutated in both WGS datasets.
The genetic linkage results confirm loci found by earlier experiments.
There were no consistent patterns of genotypic disequilibrium between loci found in multiple populations.
However, 19 loci found by sequence homology to sequences from Rfam were unconfirmed by structure homology.
