Limits...
Low-depth genotyping-by-sequencing (GBS) in a bovine population: strategies to maximize the selection of high quality genotypes and the accuracy of imputation

View Article: PubMed Central - PubMed

ABSTRACT

Background: Genotyping-by-sequencing (GBS) has emerged as a powerful and cost-effective approach for discovering and genotyping single-nucleotide polymorphisms. The GBS technique was largely used in crop species where its low sequence coverage is not a drawback for calling genotypes because inbred lines are almost homozygous. In contrast, only a few studies used the GBS technique in animal populations (with sizeable heterozygosity rates) and many of those that have been published did not consider the quality of the genotypes produced by the bioinformatic pipelines. To improve the sequence coverage of the fragments, an alternative GBS preparation protocol that includes selective primers during the PCR amplification step has been recently proposed. In this study, we compared this modified protocol with the conventional two-enzyme GBS protocol. We also described various procedures to maximize the selection of high quality genotypes and to increase the accuracy of imputation.

Results: The in silico digestions of the bovine genome showed that the combination of PstI and MspI is more suitable for sequencing bovine GBS libraries than the use of single digestions with PstI or ApeKI. The sequencing output of the GBS libraries generated a total of 123,666 variants with the selective-primer approach and 272,103 variants with the conventional approach. Validating our data with genotypes obtained from mass spectrometry and Illumina’s bovine SNP50 array, we found that the genotypes produced by the conventional GBS method were concordant with those produced by these alternative genotyping methods, whereas the selective-primer method failed to call heterozygotes with confidence. Our results indicate that high accuracy in genotype calling (>97%) can be obtained using low read-depth thresholds (3 to 5 reads) provided that markers are simultaneously filtered for genotype quality scores. We also show that factors such as the minimum call rate and the minor allele frequency positively influence the accuracy of imputation of missing GBS data. The highest accuracies (around 85%) of imputed GBS markers were obtained with the FIMPUTE program when GBS and SNP50 array genotypes were combined (80,190 to 100,297 markers) before imputation.

Conclusions: We discovered that the conventional two-enzyme GBS protocol could produce a large number of high-quality genotypes provided that appropriate filtration criteria were used. In contrast, the selective-primer approach resulted in a substantial proportion of miscalled genotypes and should be avoided for livestock genotyping studies. Overall, our study demonstrates that carefully adjusting the different filtering parameters applied to the GBS data is critical to maximize the selection of high quality genotypes and to increase the accuracy of imputation of missing data. The strategies and results presented here provide a framework to maximize the output of the GBS technique in animal populations and qualified the PstI/MspI GBS assay as a low-cost high-density genotyping platform. The conclusions reported here regarding read-depth and genotype quality filtering could benefit many GBS applications, notably genome-wide association studies, where there is a need to increase the density of markers genotyped across the target population while preserving the quality of genotypes.

No MeSH data available.


Distribution of the number of reads and variant call rates. a Number of mapped reads assigned to individual samples after demultiplexing of two 48 plex sequencing lanes. One group of libraries was prepared with conventional primers, and the other with selective primers. b Call rate of the variants in both methods of library preparation. Variants detected have a minimum read depth of 2 and a genotype quality score of 5 or greater
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
getmorefigures.php?uid=PMC5382419&req=5

Fig3: Distribution of the number of reads and variant call rates. a Number of mapped reads assigned to individual samples after demultiplexing of two 48 plex sequencing lanes. One group of libraries was prepared with conventional primers, and the other with selective primers. b Call rate of the variants in both methods of library preparation. Variants detected have a minimum read depth of 2 and a genotype quality score of 5 or greater

Mentions: Single-end sequencing with the conventional method of library preparation produced a total of 191,912,978 reads, with an average of 4.0 million reads per sample (Table 1). The GBS method with selective primers generated a total of 163,583,652 reads, with an average of 3.4 million reads per sample (Table 1). The number of raw sequence reads per individual ranged from 1.4 million to 9.1 million with the conventional method and from 1.2 million to 7.6 million with selective primers (Fig. 3a). Of the 48 samples, two individuals failed the bovine SNP50 genotyping assay and were removed from further comparison analysis.Table 1


Low-depth genotyping-by-sequencing (GBS) in a bovine population: strategies to maximize the selection of high quality genotypes and the accuracy of imputation
Distribution of the number of reads and variant call rates. a Number of mapped reads assigned to individual samples after demultiplexing of two 48 plex sequencing lanes. One group of libraries was prepared with conventional primers, and the other with selective primers. b Call rate of the variants in both methods of library preparation. Variants detected have a minimum read depth of 2 and a genotype quality score of 5 or greater
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC5382419&req=5

Fig3: Distribution of the number of reads and variant call rates. a Number of mapped reads assigned to individual samples after demultiplexing of two 48 plex sequencing lanes. One group of libraries was prepared with conventional primers, and the other with selective primers. b Call rate of the variants in both methods of library preparation. Variants detected have a minimum read depth of 2 and a genotype quality score of 5 or greater
Mentions: Single-end sequencing with the conventional method of library preparation produced a total of 191,912,978 reads, with an average of 4.0 million reads per sample (Table 1). The GBS method with selective primers generated a total of 163,583,652 reads, with an average of 3.4 million reads per sample (Table 1). The number of raw sequence reads per individual ranged from 1.4 million to 9.1 million with the conventional method and from 1.2 million to 7.6 million with selective primers (Fig. 3a). Of the 48 samples, two individuals failed the bovine SNP50 genotyping assay and were removed from further comparison analysis.Table 1

View Article: PubMed Central - PubMed

ABSTRACT

Background: Genotyping-by-sequencing (GBS) has emerged as a powerful and cost-effective approach for discovering and genotyping single-nucleotide polymorphisms. The GBS technique was largely used in crop species where its low sequence coverage is not a drawback for calling genotypes because inbred lines are almost homozygous. In contrast, only a few studies used the GBS technique in animal populations (with sizeable heterozygosity rates) and many of those that have been published did not consider the quality of the genotypes produced by the bioinformatic pipelines. To improve the sequence coverage of the fragments, an alternative GBS preparation protocol that includes selective primers during the PCR amplification step has been recently proposed. In this study, we compared this modified protocol with the conventional two-enzyme GBS protocol. We also described various procedures to maximize the selection of high quality genotypes and to increase the accuracy of imputation.

Results: The in silico digestions of the bovine genome showed that the combination of PstI and MspI is more suitable for sequencing bovine GBS libraries than the use of single digestions with PstI or ApeKI. The sequencing output of the GBS libraries generated a total of 123,666 variants with the selective-primer approach and 272,103 variants with the conventional approach. Validating our data with genotypes obtained from mass spectrometry and Illumina’s bovine SNP50 array, we found that the genotypes produced by the conventional GBS method were concordant with those produced by these alternative genotyping methods, whereas the selective-primer method failed to call heterozygotes with confidence. Our results indicate that high accuracy in genotype calling (>97%) can be obtained using low read-depth thresholds (3 to 5 reads) provided that markers are simultaneously filtered for genotype quality scores. We also show that factors such as the minimum call rate and the minor allele frequency positively influence the accuracy of imputation of missing GBS data. The highest accuracies (around 85%) of imputed GBS markers were obtained with the FIMPUTE program when GBS and SNP50 array genotypes were combined (80,190 to 100,297 markers) before imputation.

Conclusions: We discovered that the conventional two-enzyme GBS protocol could produce a large number of high-quality genotypes provided that appropriate filtration criteria were used. In contrast, the selective-primer approach resulted in a substantial proportion of miscalled genotypes and should be avoided for livestock genotyping studies. Overall, our study demonstrates that carefully adjusting the different filtering parameters applied to the GBS data is critical to maximize the selection of high quality genotypes and to increase the accuracy of imputation of missing data. The strategies and results presented here provide a framework to maximize the output of the GBS technique in animal populations and qualified the PstI/MspI GBS assay as a low-cost high-density genotyping platform. The conclusions reported here regarding read-depth and genotype quality filtering could benefit many GBS applications, notably genome-wide association studies, where there is a need to increase the density of markers genotyped across the target population while preserving the quality of genotypes.

No MeSH data available.