The parentage analysis contributes to the validation of high throughput SNP genotype calls of citrus

High-throughput genotyping is an important breeding tool to provide genome wide genotyping of germplasm forbreeding and the selection of markers through linkage mapping. However, the validation system for genotypingcalls from the automatic analysis has not been adequately developed to apply the high-throughput genotypingsystem in a practical fashion, because the marker data sets derived from DNA markers often contain missing orquestionable genotype calls. Therefore, the objective of this study was to develop validation procedures usingSNP data sets from a previously developed 384 multiplexed SNP array, named CitSGA-1, for the genotypingof Citrus cultivars. For this purpose, we initially used the manufacture’s criterion that included: (1) the callfrequency scores (over 0.9) for SNPs and (2) the GC10 and GC50 scores of samples. Thereafter, the followingvalidation procedures were investigated: (3) removal of monomorphic SNPs genotype calls, (4) removal ofNo Call SNPs, and (5) removal of SNPs with discrepancies in the parentage analysis. In these procedures, theparentage analysis could detect the genetic discrepancy between parents and progeny in the reliable criteria. The obtained reliable SNP types were also tested for the reproducibility of calls by the replicated genotyping ofaccessions on the same SNPs. The results confirm these the validation procedures, which include the design ofsamples for parentage assays and the replicates necessary to obtain the reliability of large genotype calls.