Figure 1.
An overview of the RADtyping approach for de novo codominant and dominant genotyping in a mapping population.
Representative reference sites are obtained by assembling parental sequencing reads into “locus” clusters. These sites are further classified into parent-shared and parent-specific sites for subsequent codominant and dominant genotyping. Main principles of codominant and dominant genotyping algorithms are shown in flowcharts, and more details are described in the Methods section.
Figure 2.
Evaluation of the performance of RADtyping using a pseudo F1 mapping population.
The simulated population was created by a crossing of two Arabidopsis plants with predefined SNPs in their genomes and progeny were subject to in silico sequencing together with their parents at different sequencing depths with sequencing errors enabled. De novo codominant and dominant genotyping was evaluated in three key aspects: genotype coverage (a, b), removal of repetitive sites (b, e), and genotyping accuracy (c, f).
Table 1.
Summary of polymorphic markers obtained by 2b-RAD sequencing of a C. farreri mapping population.
Table 2.
Sanger validation of 2b-RAD genotypes.
Table 3.
Codominant and dominant SNPs confirmed by Sanger-based amplicon sequencing.
Table 4.
Consistency of codominant genotyping on replicate 2b-RAD libraries prepared from two parents and ten progeny.
Table 5.
Consistency of dominant genotyping on replicate 2b-RAD libraries prepared from two parents and ten progeny.