Abstract
BackgroundGenotyping by sequencing (GBS) is a robust method to genotype markers. Many factors can influence the genotyping quality. One is that heterozygous genotypes could be wrongly genotyped as homozygotes, dependent on the genotyping depths. In this study, a method correcting this type of genotyping error was demonstrated. The efficiency of this correction method and its effect on genomic prediction were assessed using simulated data of livestock populations.ResultsChip array (Chip) and four depths of GBS data was simulated. After quality control (call rate ≥ 0.8 and MAF ≥ 0.01), the remaining number of Chip and GBS SNPs were both approximately 7,000, averaged over 10 replicates. GBS genotypes were corrected with the proposed method. The reliability of genomic prediction was calculated using GBS, corrected GBS (GBSc), true genotypes for the GBS loci (GBSr) and Chip data. The results showed that GBSc had higher rates of correct genotype calls and higher correlations with true genotypes than GBS. For genomic prediction, using Chip data resulted in the highest reliability. As the depth increased to 10, the prediction reliabilities using GBS and GBSc data approached those using true GBS data. The reliabilities of genomic prediction using GBSc data were 0.604, 0.672, 0.684 and 0.704 after genomic correction, with the improved values of 0.013, 0.009, 0.006 and 0.001 at depth = 2, 4, 5 and 10, respectively.ConclusionsThe current study showed that a correction method for GBS data increased the genotype accuracies and, consequently, improved genomic predictions. These results suggest that a correction of GBS genotype is necessary, especially for the GBS data with low depths.
Highlights
Genotyping by sequencing (GBS) is a robust method to genotype markers
In Gorjanc’s report [4], expanding the training set resulted in higher overall accuracy of estimated breeding value (EBV), even with reducing the quality of genotyping for lower expense, but genotyping quality may be more important for the prediction set
The upper panel of Additional file 3 shows the proportions of incorrect genotype calls over true genotypes and the Standard deviation (SD) of ten replicates were all less than 6.32 × 10− 3
Summary
Genotyping by sequencing (GBS) is a robust method to genotype markers. A method correcting this type of genotyping error was demonstrated. The efficiency of this correction method and its effect on genomic prediction were assessed using simulated data of livestock populations. With the reduced-representation sequencing of multiplexed samples, GBS has been developed as a robust method to discover and genotype genome-wide molecular markers [2]. Genotyping quality of GBS tends to be lower than for a chip array [4]. Low-coverage sequencing could capture as much of the variation across the genome as SNP arrays and yielded a commensurate increase in statistical power, which would be a more attractive strategy for the studies of complex trait genetics [7, 8].
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