Based on this criterion, 6 of the 8 original significant markers passed the threshold (posterior probabilities of 0.54 to 0.87).
Eight of the 12 original significant markers passed the threshold (posterior probabilities of 0.55 to 0.86), and five new significant markers were added (Table 5).
A total of 11285 markers passed the quality test and were used for GP.
In the 91 DH lines screening the Version 2 array, 1020 DArT markers passed the standard DArT quality criteria (as above).
In the 131 DH lines screened with the DArT array Version 1, 1171 DArT markers passed the standard DArT quality criteria.
In total, 1422 markers passed the neutrality test, suggesting that these markers are not under strong selection and are suitable for population genomic analyses that usually require neutral markers.
If markers passed the validation process described above for use in MAS in breeding programs, then HRM analysis was performed using a Light Cycler 96 Real-Time PCR instrument (Rosch, Mannheim-Germany) with two replicates.
All of these markers passed the Bonferroni test (Table 3) and showed a good fit with the data (see r 2 parameter, Table 3) in most cases, with better results for the General Linear Model (GML) than for the Mixed Linear Model (MLM) approach.
Subsequently, a set of 7651 SNP markers passed the filtering criteria on absence of null-alleles, disturbing additional SNP at the probe set, and genotyping interference from paralogous loci, thus showing robust performance across this germplasm (Van de Weg & Di Guardo, personal communication).
The remaining 6,000 SNP markers passing these filters were used to build the genetic maps, out of which 2,727 and 4,284 were heterozygous in Picovine and Ugni Blanc flb, respectively.
