QUALITY CONTROL OF SNP GENOTYPE DATA IN B&H TOMATO (SOLANUM LYCOPERSICUM L.) GERMPLASM: HOW FILTERING THRESHOLDS AND FILTERING ORDER DETERMINE THE NUMBER OF USABLE MARKERS
Keywords:
SNP genotyping, quality control, missing data, filtering thresholds, marker retention, tomato, gene bank, reproducibilityAbstract
Genotyping of gene bank collections is now routine, but the raw output of a genotyping run is never ready for analysis. Failed samples, poorly performing markers and uninformative loci must be removed first, and the choices made at this stage are rarely reported in full. This study quantifies, for a real tomato data set, how much of the final data set is determined by those choices. A collection of 81 tomato accessions from the Gene Bank of the Republic of Srpska, Bosnia and Herzegovina (B&H), was genotyped with a genome-wide SNP panel yielding 5,271 scorable markers. The overall genotype call rate was 69.2%, 13 accessions (16.0%) produced no calls at all, and 149 calls (0.03%) in 19 markers used non-standard genotype codes and were treated as missing. Three sets of missingness thresholds were applied in two different sequences: markers filtered before accessions, and accessions filtered before markers. The number of informative loci retained (minor allele frequency ≥ 0.05) ranged from zero to 1,110 across the six combinations. Under the strictest thresholds, filtering markers first removed the entire panel, because the completely failed accessions imposed a minimum missingness of 0.160 on every marker, while filtering accessions first retained 4,552 markers and 798 informative loci. Removing accessions without any calls as an explicit preliminary step largely eliminated the discrepancy between the two sequences. The results show that the order of filtering operations can matter as much as the threshold values themselves, and that both should be reported.
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