Combined use of phenotypic and genotypic information in sampling animals for genotyping in detection of quantitative trait loci

Abstract

Conventional selective genotyping which is using the extreme phenotypes (EP) was compared with alternative criteria to find the most informative animals for genotyping with respects to mapping quantitative trait loci (QTL). Alternative sampling strategies were based on minimizing the sampling error of the estimated QTL effect (MinERR) and maximizing likelihood ratio test (MaxLRT) using both phenotypic and genotypic information. In comparison, animals were randomly genotyped either within or across families. One hundred data sets were simulated each with 30 half-sib families and 120 daughters per family. The strategies were compared in these datasets with respect to estimated effect and position of a QTL within a previously defined genomic region at genotyping 10, 20 or 30% of the animals. Combined linkage disequilibrium linkage analysis (LDLA) was applied in a variance component approach. Power to detect QTL was significantly higher for both MinERR and MaxLRT compared with EP and random genotyping methods (either across or within family), for all the proportions of genotyped animals. Power to detect significant QTL (alpha = 0.01) with 20% genotyping for MinERR and MaxLRT was 80 and 75% of that obtained with complete genotyping compared with 70 and 38% genotyping for EP within and across families respectively. With 30% genotyping, the powers were 78, 83, 78 and 58% respectively. The estimated variance components were unbiased in EP strategies (within and across family), only when at least 30% was genotyped. To decrease the number of genotyped individuals either MinERR or MaxLRT could be considered. With 20% genotyping in MinERR, the estimated QTL variance components were not significant compared with complete genotype information but all studied strategies at 20% genotyping overestimated the QTL effect. Results showed that combining the phenotypic and genotypic information in selective genotyping (e.g. MinERR and MaxLRT) is better than using only the EPs and the combined methods can be considered as alternative approaches to decrease genotyping costs, with unbiased QTL effects, decreased sampling variance of the QTL variance component and also increased the power of QTL detection.